Boats could be similar to wagons. They hold goods, entities, and float to shore instead of always being on land. hUmans and elves could trade with your fort with goblins coming by too even if on an isolated island. So boats won't just be usable in adventure mode by the player if they act similar to wagons.... I think.
Have you noticed how wagons actually work, though? There's a reason they're a lone exception.
Their pathfinding relies upon them only having one "real" tile the occupy, in the middle. The eight edge tiles are just painted on, which is why most of the wagon can hover over the edge of a mountain when going over ramps. The connectivity map that tells them where they can go basically just looks for impassible walls like normal, then pushes in one more tile - something only applicable to a 3x3 "creature", not any other shape.
Then there's combat. Wagons are very shy and currently cease existing if they see a hostile creature or a corpse. This is a quick-and-dirty hack to keep them from crashing the game, which is why they weren't in the game for several versions before that. If a wagon was ever seen as a target (which enemies would do, because there are no vehicles in DF, there are wagon creatures made of wagon wood creature tissue) then they would start attacking and bruising the wagon wood.
Meanwhile, wagons take up no physical space, and "wear" its cargo. A ship would require it have actual cargo holds and places for crew to actually
stand so that they don't drown. Player ships for adventure mode will probably demand crew cabins, as well, which requires being capable of navigating a solid structure that takes up multiple tile of physical gamespace.
So no, wagons are totally different from ships, and would require massive rewrites to the fundamental structure of DF so that something in between a "creature" (something that has location and can move, but does not take up/block space/pathfinding) and a "construct" (something that has location and takes up space/blocks pathfinding, but cannot move) can exist.
Keep in mind, the few moving fortress parts we already have (liquids and bridges) are absolute FPS killers, already, due to the way that DF has a connectivity map. EVERY change in where the water flows causes DF to have to rebuild its own pathfinding map, which causes significant, observable lag. Until Toady switches to some different method of pathfinding, every time a ship moves, it will break the map. (This is presumably part of why ribab was trying to offer "fast travel" as a way to make ships a "static building".)