"How many universities are in Rome?"
Translation:Quot universitates Romae sunt?
Short answer: yes, special case.
in Americā takes the Ablative.
Cities and other special words (rus, domus, humus, and a few others) kept the Locative case that disappeared for most other words.
Hence Romae (which will look exactly like the Genitive Case) is locative, but America, though the ending is the same (-a) won't do that because it is not a city, but a larger structure. Therefore, like most other things you will be in, it needs the prep "in" and the noun in the Ablative (here "in Americā")
Names of cities use the locative case with no preposition.
In a declarative sentence, the verb usually comes last (subject object verb).
Ego filias habeo. -- I have daughters.
Although the copula often comes in the middle (subject verb complement).
Puer est discipulus. -- The boy is a student.
Usually the verb will come first in a question.
Suntne universitates Romae? -- Are there universities in Rome?
At the sentence level, it's mostly subject object verb, although it's a little flexible and questions often pull the focus words to the front.
At the phrase level, specifiers generally come before the noun. Other adjectives tend to go after the noun, but it's not wrong to put them before. Adverbs always go before the verb. Negations always come right before the thing they negate.
Because we want the plural. How many universities are, not How many university is.
It's not a matter of being optional. It's a matter of sometimes you must use it, and sometimes you must not use it.
The locative case is the least-used case. It doesn't even show up in many declension charts. It only applies to the names of cities/towns, small islands, and a very small handful of regular nouns, like "domus".
Using the locative means you do not use a preposition.
Here is a plain-English overview of what the cases are and how they work:
Latin cases, in English
Adjectives must agree in gender, number, and case with the nouns they modify, but they have their own declensions. Sometimes you get lucky and the adjective just happens to follow the same declension as the noun, but that is not a guarantee.
"Num" vs "quot" has nothing to do with it. Only the names of cities/towns, small islands, and a very small handful of ordinary nouns use the locative case, which does not use a preposition. All other nouns take a preposition and the ablative. Rome is the name of a city, therefore it uses the locative case with no preposition.
This has been explained on this page before.