To allow players to increase throughput of shipping without having to increase the number of cargo depots and overcomplicate the logistics in and out of them I suggest adding an "Anchorage" entity which functions somewhat like the waypoints do in the train system. This would allow additional cargo ships per cargo depot to be queued in the sea on the map.
Empty ships waiting on enough cargo to be available to pick would leave the cargo depot and move to an Anchorage to wait. Returning full ships which do not have an empty cargo depot would wait at an Anchorage until there is space to dock and unload.
The Anchorage entity itself could take the form of a cute little buoy which floats at one corner of the ship parking spot.
They could also potentially be intermediate stops between two cargo depots if internal point to point cargo shipping is ever implemented.