1.
how many hours
The question word for a length of time in hours: 何時間かかりますか (how many hours does it take?). Note that it asks about duration, not clock time — that is 何時.
2.
for hours (on end)
With も, the same word states that something went on for many hours: 何時間も待った (I waited for hours). The number is not asked but presented as large.