I can see this working and being good if ships are small. Nitpicky questions though: what would be the movement increments? One whole ship-length? 8x?
How do you plan to move players currently on the ship?
Again, I don't make mods, I don't know much about scripting or what is and isn't realistic. However the buildable elavators/trains mod seems to work very well. I thought it could use a system like that. Only rather than be controlled by commands or events, it would be controlled maybe by an item or something like that. And maybe to reduce lag, you could move the boat and people on it just barley faster than a normal player at the max, and in more than 1 brick increments, like you said.
I'm not really sure about the details, what would and wouldn't work. I guess I would leave that to whoever, if anybody, decides to try and take this on.
edit- another idea. Now this would take a lot of work and probably wouldn't be much more efficient, but I'm just throwing ideas out there.
If using bricks doesn't work, there could be a whole truckload of variations of airships as vehicles, each with different upgrades. Throughout the game instead of upgrading via building, you would upgrade via switching to a better vehicle.