I noticed the exact same problem the other day. I'm running no other mods, just testing sounds. I had never noticed this before now; but I suspect someone is going to tell us this is a bug since the beginning.
EDIT: Oh, I didn't test this yet, but I have one theory that the hearing range of that sound might be limited in distance. How close are you to the sinking vessel when listening? I'm going to set up a test where I am right on top of it and see if i can hear it.