Considering nobody else has dived in, I'll do it! But first, let me state: I am not a historian of Slovakia, Hungary, or Bohemia. This response is going to focus more on language and the problems of pre-modern standardization. So if you are looking for specific figures, laws, and dates, I will not be able to help because that is out of my wheelhouse. With that said, I hope my response below does at least answer most of your question and leave you desiring more information (and more questions!).

I'm assuming the dates you are referring to when stating "for almost one thousand years" are 1000, when István (or Štefan) I became the first king of Hungary to 1918, when the Czecho-Slovak Republic was delcared. First, I'm going to briefly dive into post 1800s Slovakia and Hungary as this is the area I know the least about. Therefore, this is the area with the most holes and which will be the least specialized. I encourage others with more information to dive in with corrections and extra information!

There was no other moment in history where Slovak language and culture were under attack than in post 1867 Austria-Hungary. With the creation of a dual monarchy, Hungary pursued a serious policy of "Magyarization," or trying to turn the peoples in Hungarian lands into proper Hungarians. This resulted in Hungarian becoming the official language in administration, education, and business. This was extensive, where by 1900 there were no Slovak secondary schools remaining. World War I complicated matters, as foreign interference and reprioritization of resources gave the Czechs and Slovaks opportunities for concessions and, eventually, independence. This last statement is (intentionally) incredibly vague, leaving out the Czechoslovak Legion, the efforts to drum up international support by Tomáš Masaryk, and changing policies of key Austrian and Hungarian figures ( or lack thereof). But alas, this was just 1867 - 1918, we have over eight-hundred years to cover! So here is where I invite others with more knowledge on this topic to comment, read articles and books, or maybe ask new questions as their own topics for further detail. I will not really be able to respond to any questions asked about 1867 - 1918 Slovakian history, due to this being a summary far outside of my historical wheelhouse.

Why was it only in the 19th century when Slovakian culture and language were under attack? There are a lot of factors to consider. Topography, religion, language, politics, trade, all played a role in making Slovakia something like a melting pot in medieval and early-modern Europe. So let's dive in!

Topography and Trade

Slovakia is dominated by a central mountainous region (the Tatra, Ore, and Carpathian mountains), and then some lowlands in the south-west and south-east (the Danubian Lowlands, or Podunajská nížina, part of the greater Little Alföld, and the Eastern Slovakian Lowland or Východoslovenská nížina, part of the Great Hungarian Plain). Much of the mountainous parts of Slovakia had prosperous mining towns, and were connected to the larger cities by the many rivers (Hornad, Hron, Vah, Danube, and Morava). This allowed transport of precious metals and ores to Bratislava, Košice, and Komárno, which could then be further crafted or traded to Hungary, Austria, Bohemia, Saxony, or the Italians. The richness of the Slovakian cities, as well as the hilly, and mountainous geography made Slovakia harder to effectively penetrate as an outside force. This may be a reason why numerous Hungarian kings opted to grant town and city charters to Slovakian mining and trading communities. Wealth from these urban centers could be carried down the rivers into Hungarian centers, like Buda, Esztergom, and ultimately the capital of Royal Hungary after the Battle of Mohács (1526), Poszony (Bratislava, or Preßburg in German). The trade and natural mineral resources made Slovakia, and therefore Royal Hungary, one of the most important and richest provinces for the Habsburgs, equal to if not sometimes more economically important than Bohemia or Silesia.

Language

Okay, so the area of Slovakia was incredibly important. Wouldn't that mean the Habsburgs would want to incorporate it more strongly into their realm by spreading German, Catholicism, and Viennese culture? And before I answer this, I would like to pose a different question: how does the language of communities change? Does one person decide to enact change? Is it a group? Is it nobody, but rather a gradual and more unconscious decision-making process enacted by the members of the community? Furthermore, when did Slovakian as a language exist? How many Slovak languages, dialects, pidgins, koines (a hyper-dialect almost akin to its own language) existed from 1300 - 1700? And finally, assuming one could work with all the varying language groups comprising "Slovakian" in early-modern Europe, what language should replace Slovakian? German? Hungarian? Which German or which Hungarian?

Now the answers: language change is rarely ever decided by one individual, and is instead the work of centrifugal and centripetal forces acting concurrently. It is both individuals, groups, and unconscious actions that determine the gradual shift of dialects that could be as large as whole regions or as small as solitary villages. There would have been many Slovakian dialects, many that would have been almost indistinguishable from Czech, and others that would have become more hybridized with German, (in the north-east) or Hungarian (in the south). And with all of this, still, what language could have replaced "Slovakian?"

Until the late 1700s and middle of the 1800s, standardization of European languages (establishing common rules for spelling, pronunciation, syntax, grammar, punctuation, etc.) did not really exist. Hopefully these questions and problems I briefly illustrated show how there was not a language to replace with one other (like some form of Hungarian), but a series of dialects, koines, and often radically different languages intermixing in Slovakia to create a constantly changing lingual landscape.