For me there are two approaches. Either have an invisible "Karma" system, or you can instead have a visible "Crime" system?
One nice thing about a crime system is that it will apply only in systems with effective security. Giving players the option to "play their way" by deciding whether they want to play only in safe systems, or take a risk and play in dangerous ones as well. This is simply a question of having some defined "crimes" in the game, and system-level policing that sends effective enforcement after players. As with the GTA series of games this ought to escalate with further crimes, most especially attacking police. Eventually the military will get involved and cross-power policing might start - who knows? - But we all understand how crime and punishment work. As a victim of crime, the better your reputation the move quickly and effectively the Police turn up. Caught smuggling last week and they finish their donuts first before wondering over the look at the wreckage and give you a crime reference number for the insurance, but if you're the guy who flew in Humanitarian aid last week through a blockade, then they turn out mobhanded, and loaded for bear. Some people enjoy playing as criminals and would find their game enhanced by sneaking around an effective police force. Other want to play in peace and quiet and would find it enhanced by some safe spaces to play in. It's a big universe, and there is space enough for everyone. The key thing about Crime is that it takes no account of whether offences were committed against commanders or content - it's all the same.
Karma has it's attraction in that it is harder to work around as the rules will not necessarily be manifest. Why do you keep getting weak rolls in Engineers? - because you keep using those weapons to grief newbies. Why do you get scanned EVERY TIME you try to dock? - because you've been ramming people. But if you don't know what these rules ARE, then it's harder to exploit them or evade them. To be honest I've suspected there is an element of this in the game for a while because I've had some catastrophic losses, which have then neatly been offset by luck in the mission boards or whatever shortly after. Maybe I've been lucky, but it would be easy to write an algorithm that looks at metrics like PVP, Criminality and so on and decides to offer a player some "luck" whenever they need it - if they're playing nicely. I'm a BIG fan of hidden rules and hidden cause-and-effect they really make a universe feel more alive. There is quite a lot of luck in the this game from PVE encounters to Engineer grinds to USS contents. The really important thing about a Karma system if that you're intentional vague about what the rules are - other than "good things happen to good people, bad things happen to bad people". No readout to tell you what your Karma is, no notifications when it changes, no explanation for your luck but huge opportunity to improve it. But the key thing is it's based solely around your treatment of other commanders - PVE or other gameplay has nothing to do with Karma.
So there you really have two systems. I'd like to see both implemented.