IMTU, when creating a subsector (assuming that I elect to get that far into the creation) I roll 1d10 for each empty hex - on a roll of
exactly 10, the hex contains a "Black System".
"Black Systems" are stars that have no worlds - at all. No gas giants, no planets -- nothing, except
maybe a very thin Oort Cloud, that is mostly rock.
Why are they left off of Nav Charts? Well, they're not, exactly - they just usually aren't typically displayed for civilian use. (Any PC with Nav 2+ gets to see where the Black Systems are).
The reason for the editing? Black Systems usually contain unstable stars that pump out massive amounts of hard radiation (as in, "hard enough to give even the military pause" hard).
As was pointed out in some canon material, hiding a major Naval Depot/Base in a supposed-Black System is pointless, as simple traffic analysis would eventually find it...
...OTOH,
minor Imperial Research Stations, pirate lairs, yachts, etc......