This isnt an issue yet as the overweight patch just came out but I can already see potential problems and new exploits.
Since no one can board ships and rafts without special permission, if I was a betting pirate, I would think that a certain eastern culture of people will start to set up raft/ramshackle sloop blockades and literally block in everyone. With no way to move other players ships all someone has to do is make a row of ships and rafts to block someone from leaving the island or prevent ships from getting close.