Transports (ships) cannot be disbanded, ever. Perhaps this was done to prevent issues with disbanding loaded transports (the code to kill the occupants first not implemented?).  Also they move at 1/50th the animation rate of armies, making sea exploration unneccesarily painful. Also, the AI has no idea about the concept of sea exploration. Relating to this last bit... there should be some thought given to what would happen if two at war transports are in the same area. The simplest solution would be "they simply cannot occupy the same tile", however, the minor downside of this is that you could tile blockade an inlet and/or harbor city.

At any rate, seems like an excellent candidate for game improvement that doesn't involve retooling deep core mechanics.