So I'm in class one day and I try to initiate a headcount of everyone in my class and so I decide to ask openly and say "How many are we?". But to my absolute shock I had some other person (along with a couple others more) telling me the question didn't make sense (grammatically) because I should've said "How many people are in the class/ take this class ?" I chose not to debate on the subject because I thought it was an American English thingy (like every thingy) but I still need to clear it up because I feel I was without error.
How many are we?
would not be a common way to say what you were trying to say, and sounds weird. I think you were trying to say something along the lines of
How many of us are there?
which is still shorter than your classmate's suggestions but sounds better.
I can't quite put my finger on why
How many are we? sounds wrong, but it definitely does.