Not sure about all boats, but Tokuno and Orc you can open all the Port and Starboard cannons and have them laid out nice in EC. All within reach.
You can then do a macro that fires all of one side of your ship's cannons, flips your ship, and fires all of the other side of your ship's cannons. This happens within a second.
You then just go through the gumps already opened in step one and reload them all and repeat.
This makes scuttling ships so fast.
And then I grab some commodity deeds and go over to the ship and commodity deed their stuff and then bring it to my ship.
This is the most efficient way I've found to do ships.