毎日、何時間勉強しますか。 Is this "What time do you study everyday?" or "how many hours do you study every day?" because:
何時間 = how many hours?
毎日、何時に起きますか。 This is asking me what time, obviously.
何時 = what time?
This 何時(nanji) compound can been read "nanji" or "itsu" or even "nandoki" according to rikai-chan but in my limited experience itsu is usually hiragana and means "when" while nanji is kanji and means "what time".