More work for Admins? NO, keep those license coming with the ships
Nerf caps = no
put them in guard systems? YES YES Y ES YES YESY SE YE YES YSE YS YE SY SEY ES YES YSE YSE! This way, Players will have to find a way to know where they are, fix their rep, make money. Even most of them will never find where those ships are since caps will be in guards, on "red" bases. And I doubt players will alter their reps just to check what is in "X" system, and they mostly don't know a thing about side progs
Bomber? Just nerf their firepower, it will be enough. Changing all their stats will take wayyyy too much time for Igiss and may break the balance even more.
Trade routes? Shut down the Sigma-13 -> Chugoku JH or try to mod a JH to make it dockable only by pirates (Could be possible,,,some kind of custom Jumpgate, but without the gate). For cardamine, ummm see below
Adding the best CD on NPC,,,and more than just 20 of them (30 is good) will stop any smuggler from going in O-100. If they are going in, and making their way out with a neutral rep, "Printscreen" Spam.