We dismantle our Longship whenever we aren't using it and have a base completed. We put the ship supplies into a chest until it's time to use the ship again. As long as you are the one destroying it, you'll get all the resources for the boat back.

But this new aggressive AI system needs some tweaks for sure. Plus, aside from Necks, the mobs should require stamina to swim for an extended period of time. They shouldn't be able to swim indefinitely and attack the ship at the same time.