1. Don't park them on top of a bunch of rocks.
2. when you leave the boat make sure its repaired 100%
3. keep a hammer in your inventory or in the boats inventory when you go on voyages

As long as its repaired when i leave it i have no issues, they take very small amounts of damage from storms (similar to exposed building pieces) but it takes several storms ( a few hours of active gameplay) to actually destroy them.