I have seen this a number of times & like you find in infuriating. Numerous times in large storms I will begin my target track only to have it foiled by them sinking. One time the ship "died" as my torp was in the water streaming to it. That ticked me off more than a little bit because I didnt get credit for the kill
Monster storms are far to common IMO. Sure a monsoon will create some doozy waves but 40' seas seem to appear with alarming regularity.
I recently started playing OM & while I havent yet figured out how to hit a ship with an eel using anything but a fast 90 it seems to me the sea state is much more agreeable & the Atlantic has a reputation for being much more dangerous (wave action) than the Pacific.