It's an interesting question that almost doesn't seem to fit this subreddit. It's as much a question of linguistics and etymology as it is of history, since it makes some presumptions that relate to modern perception of surnames.

What I want to do in this comment is to cover this kind of non-historical issues with the examples you cited — not the history of Russian surnames proper.

It seems that definitions you cite often stretch the meanings quite a bit to fit the "insulting" angle. The article at the link seems to be more for fun (Russia Beyond is an entertainment blog made to "represent" Russia in the West and create a more playful and attractive image of its culture, created and run by a Russian state information agency). Many of the etymologies in it seem to be taken from this book, Russian Surnames: A Popular Etymological Dictionary (online searchable version) by Yuri Fedosyuk. Like similar articles on entertainment websites, the article plays a bit loose with its facts, and simplifies things for effect; its theme is "surprising truths about famous Russian names", so it chooses good-sounding bits from the dictionary and leaves the rest out.

I also think there are a few problems with the premise of "so many insulting Russian names". First of all, even if we suppose names you listed are actually insulting or negative, there are a vast number of other, neutral or positive Russian names/surnames (from the number of non-church names — not Greek- or Bible-derived). Further, regarding the later stigma or perception of these "insulting" names: A) many of these names do NOT read/sound as their purported origin meanings in modern language; B) some of these etymologies may be a stretch, as these things tend to be, and then further simplified by the article's author; and C) even clearly word-derived surnames (Durov, Kozlov) tend to take on their own existence, and people do not take them literally, completely separating the surname and the underlying word (also, unglamorous meanings are not exclusive to Russian names).

For example, TolstOy does not directly read as literally fat/thick in the modern language (and in Tolstoy's time's language as wel) — it's tOlstyi (even though the underlying meaning is easy to see, the stress and one vowel are different). His distant ancestor very probably has been nicknamed "fat" (although it would have been a compliment in that era), but in count Leo's time, Tolstoys was an ancient, prolific, and illustrious aristocratic family, so the name stood perfectly on its own.

Chekhov may be connected to sneezing, but it does not sound it. Fedosyuk's dictionary states that "Chokh" or "Chekh" is an ancient name derived from the verb "chikhat'", to sneeze (e. g. the cannon-maker Chokhov). But to a modern ear, the surname literally means "of Czechs", the descendant of a Czech. It wouldn't sound like the verb to sneeze to Anton Chekhov's contemporaries as well.

Similarly, Sholokhov means "Sholokh's son", because Sholokh also was an ancient name; with that name in turn derived from an old word, presumably for roughness. Same with Bulgakov < Bulgak. In any case, it's impossible today to perceive his surname as related to smallpox or to roughness (sherokhovatost', shershavost'). At most, the non-word "sholokh" sounds vaguely alike to "shorokh", a quiet rustle. Same with "bulga".

Nabokov may have been derived from an ancient nickname meaning "lopsided" or "limping on one side" (nabokiy), but it does not read so now. If you consciously decide to read it literally, it sounds similar to adverb "na boku", something lying on its side. In any case, this was again an old aristocratic surname which stood on its own for centuries. Nabokov himself said (tongue-in-cheek, precisely because this is impossible to verify) that the version his genealogy-loving uncle preferred was that the name derived from some minor Tatar prince named Nabok.

Bunin is linked by the dictionary to two words: an old slang word "bunya", and (noted as more likely) to the antiquated/regional verb "bunit'", to roar, bellow. But this is, again, an old aristocratic line, whose official lore says that it derived from a Polish officer Bonikowski (transformed to Bunkevsky) who served prince Vasiliy II in the XV century. Whether this is true or not, "Bunin" or "bunya" do not sound like any meaningful words now.

An important exception is Gorky (his is very clearly an intact modern word meaning "bitter"): it is a pseudonym, a pen name, chosen specifically to reflect the bitter truths and realistic images of real life that the writer strived to depict.

But the more general question is whether unglamorous surnames are limited to Russian language. Surnames that reference (or seem to reference, such as Paine, which is unconnected to "pain") unglamorous concepts or objects are often heard in other language names as well; most of them don't read as direct descriptions of their bearers, or even can't be understood at all (being archaic or transformed). You don't think a man called Poore is poor, Petty is petty, or Black is swarthy. Similarly, you don't expect Hale to be especially healthy, and Osborne to be divine or bearlike. Whether surnames that resemble animals are negative or insulting is also an open question (is Horse or Hound negative? is Roach or Beetle? (even though not Roach nor Beetle are even derived from insects!..)).

Clearly meaningful names like Komarov (mosquito), Tarakanov (cockroach), Kozlov (goat), Durov (fool, durak/dura), and even Smertin (death) do not jar the listener and do not strongly invoke the word because they're surnames. E. g. there are at least three famous Durovs known to most Russians (a beloved Soviet actor, a tech mogul, and the founder of the famous puppet theatre), and no one ever thought to imply that they are stupid. Surnames can indeed sound mildly ironic (one of the most famous Russian tenors ever was named Kozlov), but otherwise not be perceived jarring at all. That is to say, to raise the problem of "insulting" names in Russian, they first have to be actually insulting.

Finally, regarding your question about warding the spirits: the Fedosyuk's dictionary in fact says that the first name Durak (lit. fool) which was widespread in XV-XVII centuries, was indeed one from a wide variety of "warding" names to protect from the thing named, or other dangers. It notes as an example a dyak (a high government official in pre-Peter Russia) signing all of his papers as Durak Mishurin.

The actual history of surnames in Russia is outside my expertise. Although your additional questions seem to be on point: peasants were indeed introduced very lately to surnames (instead of only patronyms) compared to nobility that had that distinction, and there was also a rich tradition of artificial surnames in church education.

I will try to answer some of your questions, but not all unfortunately.

First of all, almost all of these surnames do not sound like insulting or negative. When Russian hears ‘Chekhov’, he doesn’t think about old word for sneeze (also, I don’t think this one is true at all), it’s just a surname for him/her without any real meaning.

Second, a lot of Russian surnames are like -son surnames. So, Blokhin is actually son of Blokha, Zhukov is actually son of someone who was named Zhuk and so on.

Tolstoy is just Tolstoy, not someone’s son.

Some of these surnames maybe were initially created as nicknames but now Russians often do not use or do not know the words these nicknames were based on.

So, surnames like Nabokov, Bunin, Sholokhov, Bulgakov, Chekhov, or Khrushchev are almost meaningless for the modern Russian.

Gorbachev doesn’t look like something that comes from hunchback, because modern form of this word is gorbun, not gorbach. Tolstoy is quite close to fat, but still the real modern word for fat is tolstyi, not quite the same.

Also, I think that your hypothesis that some surname comes from some noun only because they sound alike is not very strong.

Komarov is not really related to mosquitos, it’s a polish surname (Komar) with Jewish roots (possibly). Nekrasov is not directly related to ugly, this surname comes from the name Nekras (extremely outdated now), and that name means ‘non-beautiful’ but such names were given by parents to their kids to defend these kids from evil: my kid is ugly and non-interesting, go away, evil spirit, find someone else.

I think it’s quite possible that some Russian nobles created funny and insulting surnames for their servants but most of your examples are something different.

I can offer the opposite of u/ayebrain 's answer: I don't have much knowledge of the etymology or culture of Russian names, but I know one relevant fact about their legal history:

Serfdom was not abolished in the Russian Empire until 1861, comparatively late by European standards. This meant the vast majority of the population were not citizens and were seen as having no intrinsic right to determine how they were legally identified. A landlord (or his agents) could choose to simply describe serfs by their physical or personal attributes - Boris the lazy, Boris the tall, Ivan the foolish, Ivan the cripple, etc. The same thing occurred in records kept by the orthodox church - e.g. births, marriages, deaths. If a serf was routinely identified by a description and this description was used in legal records, it became their legal surname, and could only be changed by petitioning the provincial Tsarist authorities.

This practice often continued after the abolition of serfdom for the simple reason that most peasants were illiterate and thus their tax records, land redemption payments, liability for military service etc. would all be recorded by someone else - often not an official agent of the Tsarist regime, but instead an informal intermediary like a village headman or an agent of the local barin. There was no real way for most peasants to resist being legally identified using a negative nickname once it had been used in enough official records.

And, of course, just like the evolution of surnames in other parts of Europe, names that were originally intended to describe one person (e.g. Smith for a blacksmith, or Johnson for son of John) gradually became hereditary, especially as inheritance laws allowed the transfer of private property from one generation to the next.

Source: Orlando Figes, A People's Tragedy