U-boats, unlike modern submarines, very rarely went underwater

I've read a lot of memoirs from WWII submariners (German, American and British - not sure if there are any Japanese memoirs in existence) and they always made test dives at the start of a trip, just to make sure everything was shipshape. Even if they somehow hadn't noticed Indy clinging desperately to the conning tower, he would have been left behind pretty early on. Unless he had gills like Kevin Costner in Waterworld.

Even a lot of the attacking happened above the water. Yes, they had torpedoes, but they also had deck guns.

Fun fact: the British experimented with subs that mounted a (fixed) 12" gun taken from a decommissioned battleship. The idea was that they would surface just enough to expose the gun and then blast enemy merchant ships. This actually sort of worked, except that the remote-firing mechanism tended to get water in it and the gun would shoot its own barrel off. And since the barrel was wire-wrapped (a technique the Brits loved) the blown-off part would stay attached and act as an anchor.