In English, present progressive is used to describe a temporary, volatile state of things. Present simple, permanent state.
In Korean, present simple is used regardless of the variant nature of things. Korean Present progressive is usually used for emphasis purpose, to put stress on the importance of a situation developing "right now".
The interrogative verb suffix + 나요? adds emotion to the sentence. It acts as a form of "tone softener", helping to make the question more gentle and friendly.
왜 우유가 끓어요? - [ Lit. Why does the milk boil? ] = why is the milk boiling?
왜 우유가 끓나요? - (Oh boy) Why is the milk boiling?
Bottom line, 어요? and 나요? have the same meaning. They just give different feel to the question.