Why does a ship having access to certain upgrade slots affect the cost of that ship? Why isn't it built-in to the cost of the upgrade? If a missile slot is worth 2 points (making this up, I don't know the real value), then why not make all missile upgrades cost 2 more points and all ships with a missile slot 2 points less?
Does this mean any ship I'm flying with unused upgrade slots is inherently inefficient?
Can someone explain why it needs to work the way it does from a game-design perspective?