Is it that implausible that the captain of the submarine might board a clearly abandoned, and not immediately sinking enemy warship? There's a possibility (Low) of finding something like codebooks, the normal tendency for people to try to get souvenirs, and then of course, the chance of raiding the galley for a sandwich.
But any sensible captain would know that a ship that is heavily listing might sink at any moment. Additionally, a sensible captain would also know that there may be potential secondary explosions from the munition on board, which would end the ship and anyone on board.
And I highly doubt a Japanese sub captain would think "hey let me get on board that listing ship to grab a codebook even though there might be US ships and planes nearby."
I don't know where you get the idea that people try to get "souvenirs." I'm sure the captain would like his sub intact better than a potential of getting something of value. Keep in mind, the Japanese captain would not know about the uranium on board. And a codebook, despite its value, was worth little to the Japanese at the time. It was not like the Japanese could send out a fleet or air wing to intercept enemy ships or planes. They were purely on the defensive by 1945.
If a ship has been struck multiple times and listing, why would there be any sandwiches left?