There are a few things to note here. First, Latin is a declined language. Most nouns have seven "cases" to denote the grammatical function the word performs. Five of these cases cover most situations: Nominative case (the subject in a sentence); genitive (possessive), dative (indirect object, plus use as object with some verbs and also with some prepositions), accusative (direct object, plus use with preposition), and ablative (a very flexible case, including use with prepositions and a variety of other uses that would be an article all their own). There are also the vocative case (used in addressing someone - "Et tu, Brute" uses it) and the locative case (to denote being in or at a place.) Most nouns have singular and plural forms. None of them form plural forms by simply adding an "s" or "es" onto the singular form.

Latin nouns are grouped into 5 declensions (or groups of nouns that have similarity in the endings they use for the various cases). Of those, second, third, fourth, and fifth declension nouns can end in "s" in their nominative singular form (although not all of these nouns end in "s"). They all look a little different in the nominative plural. Here are some examples, along with the plural:

Second declension: gladius ("sword") (singular), gladii (plural); servos ("servant") (singular); servi (plural) (This declension includes the stereotypical Latin nouns ending in -us).

Third declension: mens ("mind") (singular), mentes (plural); ars ("art") (singular), artes (plural)

Fourth declension: fructus ("fruit") (singular), fructus (plural); manus ("hand") (singular), manus (plural). The difference in the two forms is that the plural uses a long "u".

Fifth declension: res ("thing") (singular), res (plural); dies ("day") (singular), dies (plural). In these cases the two forms are

There are also plural endings for all of the other cases. For instance, for "gladius" the plural forms are gladiorum (genitive), gladiis (dative), gladios (accusative), gladiis (ablative).

So now about Latin loan words in English--when did they lose their Latin plurals? The answer is, it depends. A lot of words in English have Latin roots. Some came into English in the early stages of the evolution of the language in the Middle Ages, and often quickly lost their Latin plurals as English evolved and they became common words in English. Others came into the language via one of the Romance vernaculars, usually French, so by the time they made it into English, they had normally also lost their Latin plural forms. We do have loan words in modern English directly from Latin, however (particularly scientific and legal terms) --and some of them have retained their Latin plurals and some have not. For instance, there is the word "alumnus", usually meaning a male graduate of a school or university. The plural "alumni" is still widely used, much more than "alumnuses". Slightly different are words like "index" and "matrix", where you will hear both the Latin plurals "indices" and "matrices" and the English-style plurals "indexes" and "matrixes." And then you have words such as "virus", where almost everyone in everyday discourse uses the English plural "viruses" rather than the Latin plural "viri". What this points out is that there is no standardization in whether a Latin loanword uses the English or the Latin plural form--it depends on various factors, including where/how and by whom the word is used.