The Flare Gun already comes with twice as much ammo as the ship system, and is a whopping 1 OP (zero if you have Optimized Assembly). It's super cheap; it shouldn't be an incredible point defense weapon on its own (seriously, it can block weapons fire and do EMP to ships), so the downside is that it uses ammo.
Same story with the Flare Burst Launcher. It's an extremely good PD weapon - the best anti-missile weapon in the game. Unless your enemy shoots from point blank or uses rockets, it will attract and destroy just about every missile fired at you. The main downside is it has limited ammo.
You shouldn't need to ration these weapons much; they have a custom AI that uses them smartly and doesn't waste them trying to shoot enemy ships.