My suggested solution is in a similar spirit.
Make it so that a ritual skull is needed on board your ship as well while in the "fog" of the fort. I would also try to find a way to discourage people from shooting out and swimming to the island, so maybe your ship is needed in the vicinity as well in order to actually reach the island (like shores of gold). Maybe hard for Rare to execute this portion because the fort location is so centralized, but that is how I would have done it.
If you don't bring a ritual skull, you will take holes like sailing through the red sea, and so would function very similarly to the shroudbreaker.
It would also make for some interesting PVP, in which the skull can be stolen off another players boat to start sinking them (maybe a bit OP with the current boarder meta).
Players can either spend a minute to go get one the old fashion way, or can buy one from the outpost. At least it would put some skin in the game for those crews, and if the attacker were to sink, would enable the crew doing the fort to do it again if they wish.
Edit: I don't think preventing boats from joining the server with an active fort is the best idea, due to the risk of server alliance farming. Rather I would like to see boats have to invest more to attack the fort. The fact the attacking ship has limited supplies isn't really all that relevant because sinking boats has more to do with boarding proficiency than supplies (while surviving at the fort does have to do with having plenty of supplies), and attacking boats can respawn with fresh supplies. It also doesn't factor in the fact that multiple ships can be attacking over the course of the fort, or just trolling by detonating stronghold barrels / hiding at the fort etc.
All part of the game, but the question is whether it should be to the extent it currently is, or is there a more fun (for everyone), more sensible way. I'd personally like to see the fort activated more often in servers, so requiring ships to bring a ritual skull with them to engage in the fight is a great way to ensure the fort can be activated again fairly quickly.