Have a look at some EVO (or EV) TC plugs to see how they deal with the problem. The Frozen Heart springs to mind.
In my limited experience (with EVO), systs are easy to get rid of but - spobs are the difficult ones. As already suggested - just put the systs somewhere that you can't get to.
With spobs you must make sure that they cannot be landed on (set the appropriate flags in EVO, don't know about Nova). Otherwise they will turn up in mission computer cargo missions (or indeed any mission that has random destinations). Look at some bad TCs to see the problem.
Outfits and ships need to be overwritten such that they don't turn up either. The easiest way is to give them a very high tech level (and not one that is used as a special tech level on some planet).
You should also worry about nebus a little (they are only cosmetic after all) and missn's.
As this is based on my (limited) EVO experience some of it may not apply to Nova. I leave it to knowledgeable people to correct any misperceptions I may have created.
Its amazing how "tsk, tsik, nik" can mean anything from "There's a bomb in the bus, get help!" to "I'm hungry, feed me"
In case of ambiguity about anything I say - choose the nicest interpretation.