My ships are usually destroyed by various types of enemies (everybody seems to like to attack them except deers). So maybe something is coming to your docking place and destroys the boat while you are not there? Is the docking place of the ship within the working radius of a workbench as those prevent despawning of dropped loot/items (otherwise, the items will usually despawn within a few game days - and i think they will despawn even quicker in the water than on land)?