I was looking at some random stuff on DTRPG yesterday and it dawns on me that technically Rifts probably qualifies as a game with enough submarine shenanigans going on to deserve mention, although I sure wouldn't recommend it. They've done a number of splatbooks over the years dealing with nautical stuff, including parts of Atlantis, Underseas, Lemuria and Coalition Navy plus whatever other stuff is hiding in other books or the countless Rifter issues. Almost certainly more pages spent on this stuff than anything out there except Blue Planet, and even that's probably close.