Like in real life, boat should be used to transport people but most important large volume of goods from long distance (like wood and ore from the north, grain and animals from the south), maybe not as fast as cart pulled by horse, but in a more secured way by sea. The only risk is to cross a pirate ship full of bandits or an enemy guild on boat or on shore throwing a rain of arrows.
Boat construction should be in carpenter skill and not a new skill branch, then, no need to grind and craft thousands of useless boats to level up. There should be different class of ships, like small transport ship at lvl60, medium ship at lvl90 and large warship at lvl100. Carpenter would love it and it will give then more jobs to do.
Of course crafting boat should be very hard and expensive in resource and need to be well balance, it will need to add much more crafting recipes in different class of skill, tailor and farmer for linen sails and cords, forging for metal parts, carpenter and forester for wooden parts.
but first thing i suppose is to modify the game engine to get all this "sea game mecanics and physics" work as intended.