Try this, before you change the loudness of the file deactivate the FotRS mod and any other mod you have activated.
Install Silent 3ditor and you can turn those sounds off or down yourself. The file you're looking for is in the Sounds folder and it's called amb_SubmarineInterior, load it up using the
sh thingie it's a type SDL file and it looks different to all those sound files.
Inside the Silent 3ditor the file is called Ambient.Interior, turn it down to about 50 and save it making sure that you are saving it inside 100_FalloftheRisingSun_Ultimate_v1.46_EN and that should sort it for you.
If that above wasn't clear enough for you I'm sure someone will reply with roughly the same instructions but better worded.
Ooh, Mr Randomizer is quicker than I am.