Most submarines that were sunk as the result of combat had their hulls punctured, which would allow any battery acid to eventually flow out of the hull. The greatest threat I've heard of is unexploded ordnance, fragile structures that can break or collapse, and the gret depths some of the boats lie in.

Showell's book outlines a morbidly humorous incident about a commander making a critical error when flushing the toilet. (the 'thunder boxes' were rather complicated to operate) The commander's offering, plus plenty of sea water, was shot back in his face. The seawater that flowed in got into the batteries, chlorine gas forced the sub to surface, and it was lost.