Not trying to dictate how anyone should play, but I know lots of players dismantle their ship anytime they aren't traveling in it.... Make landfall then set up portal (if you use portals), then break down your boat and save the materials for when you need to use a boat for transportation again.

Mobs will seemingly go out of their way to go out into the water to destroy ships, and they don't experience stamina or drowning, so they will certainly get the job done.