Okay, so while I was starting up a new fort from a new version of the game (I've been on an educationally-related hiatus from DF), and I noticed that the names for the categories used here an there were... I'm going to be blunt, extremely bad Latin. So, I figured that since part of my aforementioned educational hiatus was because I was taking amongst other things, Latin, I figured I'd volunteer to help out a little by giving more... accurate Latin translations for the categories. I understand if you don't want to use these for any reason at all (I could see it being hard to see what's what without any knowledge of Latin being a factor), but I'm going to give them to you so you have the informed choice as to use them or not. That said, if anyone has better translations than mine, please put them forward; even if they don't get used in the game, I'd love to see them.
Unless you were writing all of these in Italian, in which case just ignore everything here.
General:
You keep using the word "Dwarvica"... it doesn't work in Latin, and for multiple reasons: firstly, there is no "W" in Latin, the sound that makes the "w" sound is actually "V", and it should be noted here that "V" and "U" are interchangeable in Latin, but are usually used by modern speakers, the actual Romans made less distinction, for when the letter is being used as a consonant or vowel respectively; meaning that a more accurate Latin-ish word would be Duarvica. Secondly, is the fact that Latin already has a word for "dwarf": pumilio (which can also be used to people with some form of dwarfism), or nanus (which refers exclusively to mythological creatures... but also can be used to refer to gnomes), so neither is really correct as per my understanding, but I'm going to work with pumilio out of personal preference.
Workshops
Manufactura Dwarvica -> Fabricae Pumiliorum. Manufactora is a real adjective meaning "hand-made", (Feminine singular or neuter plural), it does not have anything to do with the place in which those objects were made, no matter what the Techpriests say on the matter. The actual word for a workshop is "fabrica", since this is about more than one workshop, it'll be plural. General complaint as to "Dwarfica"; replacing it with the genitive plural of pumilio.
Sanctorium: The word you're looking for is "sanctorum", no "i". But sanctorum is the genitive plural ([noun] of the holies), so you might want to use "sancta loci" (holy places).
Bibliotheca Dwarfica -> Bibliothecae Pumiliorum. Bibliotheca is arlead correct, just changing it to plural, and my general complaint as to "dwarfica" and again in genitive plural.
Scriptorium: Not a category, but this one is not incorrect at all, in fact, it's perfect just the way it is. Kudos.
Academica Dwarvica -> Scripta Pumiliorum. Academica isn't a word, but "Academia" refers to either Plato's school of philosophy, and they don't qualify as a institution of higher learning; the buildings here are studies, not academies. The Latin word for a study (the location, not the concept of studying) is scriptum with the plural being scripta. If you really want to imply "academy", then the word you're looking for is "academiae". General complaint with dwarvica.
Scientifica Dwarvica -> Laboratoria Pumiliorum. I'm not sure what you mean by "Scientfica", but these are all laboratories, so I'll just call them such.
Machinarium Dwarvica -> Machinae Pumiliorum. Machinarium doesn't seem to be a word, and I can't find any word meaning anyting along the lines of "a place where machines are built", so I'm just going with machina.
Fernaces
Manufactura Dwarvica -> Fabricae Pumiliorum. Same reasoning as above.
Manufactura Metallica -> Fabricae Metallum. Same reasoning for Fabricae, but metallum is just the nominative singular for "metal".
Manufactura Arma -> Fabricae Arma. See above.
Manufactura Upgrada -> Fabricis Amplibus. There is no word for "upgrade" as best as I can tell, so I took the participle of Amplio to get something along the lines of "Factories (for) upgrading"; I have them set in the ablative because the factories are where the upgrading is taking place, and the adjective has to be in the same case as the noun it's modifying.
Academica Magicka -> Scriptae Magiarum. See above for reasoning as per "academia". Magicka isn't even a word in Latin, but from phrasing I'm assuming you're referring to something along the lines of "Schools for teaching magic", so "Studies of Magic" works for that in my opinion.