Actually, this is not quite the case. Japan deployed five midget submarines to coordinate with the air attack. One was sunk off the coast a few hours before the air attack, leading to a heightened alert level in some quarters, at least. It was beached and the US captured it.
The crews of the submarines were quite famous, in Japan:
In addition, after the war, an aerial photo taken by one the Japanese pilots became available:
There is a dark block in the mid-harbor area at the start of one of the torpedo tracks. Some believe it's the conning tower of one of the subs. USS Oklahoma was hit by several torpedoes, and one appeared to be much larger (more explosive force) than the aerial torpedoes.
Ron "Climb Mount Niitaka" Wanttaja