One thing that always irked me is that you don't get any money for killing pirates. I mean, let's face it; pirates are hated by everybody. Even though you'll happily raise the bounty on someone to encourage pirates going for them (possibly instead of you), you'd also be elated to see them hung. And so would the trade guilds within your empire.
So my suggestion is to make pirate ships worth a bounty - perhaps the scuttle cost of the ship type, in credits only? Not only would it make sense, it would make the mass pirate suicide swarms more bearable.
Downside: Okay, thirty pirates are invading my sytem, stupidly flying into my guns.
Upside: That's gotta be about 2,300 credits worth of pirate booty!