For Raft and Karve sized boat houses, you can use the large double doors but of course this leaves a gap large enough for something to swim in. Solution is to build a single 4' core wood pole midway in the gap.
Of course, when entering or leaving you have to demolish and rebuild the pole along with opening and shutting gates. Not sure if something similar could be worked for longboats?

What I end up doing mostly is build a loading and unloading cargo/repair dock a bit away from any base so it doesn't get attacked in a raid. I then park my ship out to sea as far as I can safely swim, jump off, swim to dock, and go about my business till I need the ship again.

Hopefully someone has a better solution?