I also thought about that. But the DDF has the answer, like everytime. Dark Systems, Planets and Deep Space Signal Sources. This thing could easily build on top of the current planet structure because they don't change anything to the current system structure. Its a complete new layer of content, on top of the current star systems. The DDF also describes how this would be done:
There needs to be a scanner, that scans about 10-50 ly around your current position(depending on scanner quality). The scanner gives back a heat map result with different resolution(depending again on scanner quality, to make some especially precious objects only be scannable by the best scaners).
Then you can send hyperspace probes to this regions to scan them and answer with data about the target region. If they find something they are being used as a FTL Anchorpoint you can warp to. Then you can scan the system with in system scanning equipment(as described in the DDA). The things you can find could be:
- Planets to scan(and later land on),
- Black Holes,
- Asteroid Belts,
- Thargoid bases(when they finally arrive),
- Ancient Space stations and other things of completly unknown origin who hint to some precursor alien races.
- Ships stranded in the void in cause of a hyperspace malfunction(both: wrecks and still alive in need of some fuel).
- Pirate hideouts
- Unknown Artifacts
and so on.
Some of this thing would be random generated/scripted like signal sources. Some of them are persistent like normal star systems but hidden and more preciours because completly unexploited.