What normally happens when the weather kills a ship is that is catches fire first, depending on the mods you have, where ther'e fire there's smoke
I've never seen anything larger than a Coastal Merchant/Tramp Steamer sink itself in bad weather. The Luftwaffe doesn't come out much when it rains so I doubt it was them.
Don's suppose you had saved just before you went after him? If you haven't progressed too fare you could always go back in time and take a look at him with the external camera and see who else is about.