Something broke your ship (either a mob or waves bashing it into rocks), then the items despawned. Nothing despawns inside workbench range (though mobs will destroy workbenches). Outside workbench range and in water items despawn VERY quickly (I've tested it, throwing stuff into the sea), but I don't know if that is true if also within workbench range.

I always kill any nearby mobs and put down a fire and workbench whenever I park a boat. Just in case.