I had an email discussion about this recently and I didn't see any posts of mine in the threads Footkerchief linked (though I've said it elsewhere), so I figured I'd say it again. We'd like to have larger ships, something 16x5 with a 3 tile wide deck and multiple z levels would be fine. And yeah, there are a few problems.
With the improved sieges (sometime soon after this release, likely) will come a different and more properly supported notion of a moving vehicle (say, a siege tower), likely as a set of tiles handled something like constructions, but with the ability to move as a unit (along with any creatures or items in their tiles).
Now, boats can move along any heading in a near perfect approximation (over over up over over up etc., maybe using the guts of the standard line drawing algorithm, etc.) but the main issue is displayed facing. There are issues with any rotation idea I've heard of that does more than 4 directions. The shearing row by row idea in alfie's post for example has issues with flows coming in along the diagonals (especially in a multi-story ship), and that there's still going to be a fundamental flip once you hit 45 degrees anyway. The flows might be plugged up with temporary tiles along the new diagonals or something, but that might lead to temporary floors for items that then disappear or something. There are a lot of issues.
There's also the idea of just using 4 directions for the boat (it can move in many more directions, but it can actually only sit in 4 directions). This leads to teleportation and displacement problems, but these aren't necessarily deal breakers, especially if you add a requirement that the ship must have a free space underneath any tile (so water critters and swimmers can just be pushed down a tile instead of teleported across the ship, which isn't so different from what would happen if you get run over). You can also deal with the ship flipping back and forth between two directions by instituting some buffer versus the actual facing, so that crossing from 30 degrees to 45 doesn't change you from east to north, but you have to actually get to 60 or so first. Then once your ship shoots up to north, you have to go all the way back to 30 to get it back to east, which gives you a 30 degree difference so you can't just flip back and forth. Flips need to be minimized not only because they are ugly, but especially with issues like wrestling and stuck-ins, they can be fundamentally messy and game-breaking (say a guy on deck is holding a crew member who is dangling overboard while a sea serpent is chomping on the dangling guy's leg and then the boat turns, and the sea serpent is hooked to a post underwater, etc. -- you'd probably want to break the chain of creatures and buildings at the weakest link, but it might be a net not a chain, etc etc etc).
Anyway, things are possible in dwarf mode, but the idea here was more for adventure mode and the necessity of boats there. If boats never make it into dwarf mode it wouldn't particularly bother me, since we are talking about dwarves, but I wouldn't rule anything out. I'm starting from an adv mode perspective here though, since it would obviously be a lot of fun to do things like epic voyages and piracy.