Maybe they could do it something like how wagons are done now (assuming it it would be an accessory to fortress or adventure mode, and not another mode entirely, as some would prefer). Have a large, multi-tile creature that multiple dwarves can be mounted on at the same time, and attack from, while carrying large amounts of goods, and perhaps have its swim speed linked to wind speed like power generation in windmills. How to get the dwarves to utilize the edible goods while on a long trip so they don't starve could be an issue (although I'm not sure it would be). Heck, you could have different types of ships where the swim speed isn't linked with wind speed (boats with oars), or give them inherent ranged attacks to simulate cannons or ballista or some such. Ramming would just be the "push" attack with an appendage similar to a bronze-plated battering ram.
Of course, it would be grand if Toady or a modder could figure out how to make moving, floating floor tiles that carry what is on them without it falling off (as would be the case with floor tiles that disappear and respawn to give the illusion of motion), and an epic feat from what I know of the subject (which is, admittedly, very little). This would of course be a truer representation of sailing that just riding a swimming creature, and I imagine would open up more avenues for exploitation.