So the answer is basically two parts.

1. Is that not all of the harbor was deep enough for Capital ships. It required active dredging to keep it navigable. So the SE quarter of the harbor was generally deepest, but even then had a dredged channel and outside was shallower. Everyone remembers the potential danger of Nevada blocking the entrance but blocking the channel could have been just as bad.

2. Air dropped torpedoes don't run perfectly level. The biggest problem is that when dropped they dive down deep before leveling out at the set depth. That initial dive was the biggest problem to be delt with.