For the damage while "parked", it's possible to avoid.

As mentioned, make sure your boat isn't near rocks, or rocks that get exposed during storms as wave heights change.

I built my boathouses with stone typically, and put core wood posts/beams on the water/stone edges as 'guides', kind of like you would see in a real-life wharf where tides are a thing.

Even in storms, where the parked boat is travelling up/down a lot, no damage occurs.

The other option is building your boathouse 'inland' a bit where the storm waves won't reach.