The navigation system would probably need to be enhanced with Computercraft to get it to be reliable at all, and that's probably the most challenging part.

But the logistics part I think really isn't too bad. If you have 2 different docking blocks, you can use one to load all outgoing packages and sort them into 1 inventory per port (using filtered brass tunnels). Then you can have some kind of system using colored lasers or some other signaling system that can give a unique signal to each port, which would enable the corresponding inventory on the ship to start outputting packages addressed to the current port.

On the port side, you can make 1 simplifying assumption: all outgoing packages will be sent to their destinations by any given ship that docks at the port. If that assumption is true, we may simply have a buffer of packages that all get sent into any ship that docks, no questions asked. Beyond that all that's necessary for a port to have is a unique identifier readable by the ship, which could just be a colored laser or even a specific block in a unique location.

Without the simplifying assumption, (say in a system where our port has packages addressed to port A and port B, but a ship might be docking and only be scheduled to visit port A) then there needs to be a system that can recognize the ship as well as the ship identifying the port, and that system must then determine which packages are allowed to be routed to the ship. That gets a lot more complicated.