So, only one librey Bonus, they don´t stack?
Why would they stack? If you have multiple libraries you can only purchase the same collections for each of them, meaning with multiple libraries you will only have (in the
best case) multiple copies of the same books. In which situations do multiple copies of the same books give an additional bonus? Would you learn something new from a second copy of the same edition¹ of the Encyclopedia Galactica, which you would not be able to learn from reading the first copy of the same edition of the Encyclopedia Galactica?
Clearly in a university library (and other public libraries) it often makes sense to have multiple copies of a book, as in that case multiple students (or customers) can read the same book at the same time, but they are not able to get additional information from a second, third or xth copy of a book (which they would not be able to get from the first copy) - books on the same topic (with a different focus and different ways of explaining things) are entirely different thing (ie. depending on the recipient or reader one form of presenting information might mean that he/she learns more than from another form of presenting more or less the same information).
It is already interesting that just adding bookshelves (with copies of presumely the same books) do give an additional bonus.
The only thing that does not make so much sense is, that not the highest boni is taken, but the bonus from the library with the highest room number (for the stat gain of npcs during the midnight calculations).
Stacking of boni (from libraries/collections) would only make sense, if there were more collections to purchase and not all of the collections would fit in the same room (ie. you can only fit n collections into a library room, but there are k different collections, with k>n) and you would not be able to purchase the same collection a second time (at least as long as you still have the collection in another library room).
And if you do not believe me, just look at the html code in the passage "Rooms" (search in the html file for the string 'name="Rooms"' without the single quotation character ' and then search further for the string 'LIBRARY EFFECTS' again without the single quotation marks - or just search for 'LIBRARY EFFECTS' still without the single quotation marks) and read the code yourself.
¹) Of course from a later edition of the Encyclopedia Galactica you might be able to learn something new, ie. about the marketing department of the Sirius Cybernetics Corporation.