I think there's a few different ways they could be balanced:
Similar to what psykoe has said in another thread, I think the ghost ships are too aggressive. I feel like they should be slower than all other actual ships, so that you actually have a chance to escape from them if you wish to. Or, like psykoe said, simply make them non-aggressive until fired on.
However, if you do decide to keep them hostile but slow them down, it might be a good idea to make their cannon range further than any player ships so that they can't be cheesed. That way, people who want to fight them can, and people who don't can actually avoid them rather than losing hours/days of work thanks to something they could do nothing to stop.
Finally, I also think that ghost ships should be limited to one or two per zone, IF ANY AT ALL. Having fewer of them, along with the changes above, means that you can ramp up the loot quality and scale their health however you like, while also adding another layer of gameplay in terms of having to actually find the ghost ships to begin with. It could end up with people from different companies working together to search for them in multiple ships, and then taking them down together like raid bosses. Personally (especially from an MMO standpoint), I think that sounds much more fun than having them flood every zone.
I really hope you take these suggestions into consideration. I've been enjoying the game a lot already, but I really do think Ships of the Damned need some changes.