Why doesn't the verb 'be', here 'is', agree with 'stops'? What kind of
grammar is "how many stops is it..."?!
By the same analogy, can I say "how many apples is it in the fridge?"
If yes, how is it different from "how many apples are there in the
fridge?"?
Consider this imaginary conversation:
How many apples are there in the fridge?
-- There are more than you would expect. You will never guess how many there are!
Six?
-- No.
Eleven?
-- No.
How many apples is it, then??? Just tell me! I don't like this guessing game.
This idiomatic example shows that, semantically, "are there" asks for the number of something, whereas "is it" presents the answer to the question as being in a different category from "number", that is, as being in the category of "what-I-don't-know" or "information-I-need".
The difference between dummy "there" and dummy "it" is in the degree of abstraction. The locative dummy is the more tangible of the two.
So, the idiomatic question "How many stops is it before we get off?" is projecting to the listener the idea that the questioner would like to know a particular fact. Agreement in number is not relevant to this form of dummy "it".
The locative dummy being the more tangible, number agreement is more relevant, and therefore "How many stops is there?" raises grammatical red flags whereas "How many stops is it?" does not.