I'm not sure, but I think your NavMap would show a sunken ship icon, whether it sinks in a storm, from your actions, or any other manner, including an airplane bombing / depth-charging the 'target'. The game itself does seem to have an issue though, with "shutting-off" the engines of sunken vessels, and I have also found sonar evidence of ships, including in areas that are very, very deep water, in which a sub should not be able to pick-up the signal - seems to me, anyway. As far as I can recall (what did I have for breakfast?), stock & all mods do the same. CapnScurvy, or one of the myriad other more experienced modders would have a better perspective on that...
