So we had a brainstorming session in the OYT community chat and I think I finally came up with something. And, of course, it is obvious.
Contraserrene once again is brilliant and creative at the drop of a hat, although this time it was not his idea I stole.
The main sail of the model ship will contain hidden markings that serve as the key to the map. The map consists of the knotholes and other wood patterns on the hull of the ship. Some fine filigree along the ship's railing serves as a coordinate system that is detailed on the sail. So, you decipher the sail, discover the markings on the boat, and match them up to find the sunken ship.
Of course, it is not so easy. Because the valley is no longer flooded, you have to look up to find the islands and landmarks that were visible from the sailing ship.
The actual construction of the cipher will come later.
Perhaps the mast, maidenhead, or the pole that juts out from the hull above the maidenhead is detachable and bears a key on the hidden side. This key opens the chests in the sunken ship and disables the traps on them.