I just had a Gjall blast my longship. I got to the wreckage just after I finished it off, and there were crates there, and the ship parts were there (nails at the bottom, of course), but some of the items in storage were in the water, not in crates. My assumption was that some of the crates were destroyed in the conflict after the ship was sunk.

What you're describing seems pretty short for despawn, but I don't know what else it could be.