Well, without knowing what destroyed it, it's impossible to say, beyond a generic 'park your boat better' comment. Generally if you're not physically in the boat, I don't think the water alone can do anything to it, no matter how stormy it is, but if it's close to the shore, all sorts of things can happen. My guess would be that either enemies destroyed it, or it was close enough to the rocks that rough waves caused it to flip over.

Either way, if it's in shallow water, you DO get 100% of the materials from it, unless they despawned.

So
-Don't park too close to the shore, or if you do, make sure it's in shallow enough water so that the materials that sink are still in reach.
-Don't leave it unattended for too long.