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For the wheels and animation I had a thread discussing moving wheels for chariots and carts, etc. Seems like it would take some in-depth knowledge of hot to animate for NWN to do so.
For the walkable decks, I had a placeable bridge walkable by placing it a little bit above a tileset bridge. If you could find a raised tileset feature of the right size, you could place the ship on it and surround it with some placeable water pieces.
The best solution would be something like what they did for the flying hak that was done a while back with invisible ramps and raised areas. If a tile creator made some water tiles with large areas of invisible floors above the water level, the ships could be placed to align with them and you could walk on deck. It would also be good for flying over the water effects.