one day seems too fast to despawn the mats, though.
what usually happens is enemy attacks break the ship, the swamp is prone to leeches in any water including the ocean for a long way out. Attacks can move the ship, slightly, so you have to check a radius of where you left it. Once broken, you normally have some time before it despawns.
adding a workbench etc can reduce spawns and attacks as well as preventing despawn, but the enemy are just as likely to smash that as the boat. The best way is still to pack it up somewhere safe and rebuild it when you need it.

Getting stuck with no way out is, as you noted, more tedious than a challenge. The key is to avoid having that happen, via portals usually. When I explore a new shore, I always set up a small camp there... a bench, a chest, a portal, sometimes a fire and cheap comfort like deer rug, some shelter and defenses so the portal stays intact... stow the boat in the chest and off you go. If the island isnt interesting, you can pull up and move on. If it is, you have a base to pop to next time straight from home. If the new place has ore you need, I will also level out the beach terrain to make boating easier. Its now a one way trip, portal home to camp, get ore, boat back home, repeat as needed.