I think the Moonbeam’s ability could be easy to keep track of. You could purposely wait until the end of the turn to shoot with her, or simply give up in situations where you needed her to take actions before other ships. Although some weirdness could occur if she was the last ship you shot with on a turn, but long before your turn ended so you might forget to apply the bonus. XD
Not a big fan of high-cargo gold running submarines, even with those negative abilities. It’s just such a defensive keyword that I could see them being a bit OP. In addition, most 2 masted subs have 2-3 cargo, and I like keeping things somewhat in line with what has been laid out in terms of reasonable cargo holds by ship type. I like to think they did that due to how much technology would be required to even have the MI subs in an “Age of Sail” environment – things would be quite cramped on board, with nowhere near as much room as the cargo hold of a sailing galleon/etc.