There’s definite appeal to having additional ways to gain points, especially when it promotes directly interacting with other ships instead of just racing for the most gold.
Points for capturing opposing ships a very good one, although I think some sort of fixed rate is better than basing it on the value of the ship and/or its crew. Likewise with sinking ships or eliminating masts. Instead of being based on what you hit, I’d rather it be a straight value, like 1-gold per mast destroyed, 2 points for a crew, and 5 or 10 for each ship sunk. Whatever the rates are, it shouldn’t be so much that it offsets any gold picked up, because that should still be the priority.
Points for what you have remaining is already kind of addressed by having a build total for your fleet, but making that a major part of end game scoring could lead to some weird self-preservation / turtling tactics. A player might decide to leave an expensive ship docked at home purely for the point boost. There would of course be a break-even area where the points hoarded at home would be offset by having less to work with elsewhere, but if both/all players are doing it that point is much lower than if only one does it, and then effectively you’re just playing the game at a lower fleet total – which is maybe a better way to handle it.
Instead of getting bonus points for what you have left at the end, you get bonus points for how far you were under the fleet total at the start. You still might end up playing games where everyone is playing at a lower total, but that’s much more clear up front, and you never have to wonder which part of the opposing fleet is actually active and what’s there just for the points.