One issue that has always plagued Valheim ships is that the raising and lowering of waves suddenly, causes damage to ships, and is especially more evident during times when the player sleeps to pass time... The boat raises up with the high wave but then the water drops out suddenly, and the ship "falls" a short distance to land in the water, and that's what causes the damage.

Enough times of this smaller "fall" damage, and the boat breaks apart.

To keep your ship safe during long periods of not using it, manually break down your ship, in SHALLOW water, to retrieve all of your materials back, and simply re-craft a new one as needed.