No mods, vanilla... Also what I forgot to mention that when I lost my first boat I left some iron scraps there in the boat inventory. When I noticed my boat is missing later I went to look around. All I found was a crate floating on the water named "Cargo" and had all the iron scraps in it. No materials from the ship though...

Is it possible some gremlin swam in there all around the fortification, destroyed the ship and then swam away. Maybe this game is just trolling me