3

How should I say:

Why there is only one student there?

or

Why is there only one student there?

3

According to the basic rules of English question formation, the word that comes after the question word (those are words like why, what, where etc.) is either one of the two auxiliary verbs (to do and to have), a modal verb (would, might, should etc.) or one of the numerous forms of the verb to be. That's why, strictly speaking, only the second sentence is grammatically correct:

[question word] [auxiliary verb/modal verb/to be verb] the rest of the sentence?

Why was there nobody in the room?

The first sentence as a question is still technically possible, though. You'd most likely hear this in a situation where somebody first uses it as part of a regular declarative statement and then you repeat it with a rising intonation to indicate a mild surprise. In English, as is common across many European languages, a rising intonation is all you need to turn a declarative statement into an interrogative one. A short example dialogue:

— He wants to know why there is only one student there.
— Why there is only one student there? Really? Is that what he wants to know?

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