As you may have seen I've attempted to create a "near Earth" 3D-based map in another thread.
Using "bubbles" - Yes that would work - once you go with an abstract "flowchart" like map, you can easily create arbitrary groups - let's call them Clusters - to remove unneeded detail.
You still need to first map out all those stars to know WHAT you are abstracting, though.
In the end, however, I returned to a flat map, and at a larger scale. I agree with barrataria, in that creating a detailed 3D map of anything bigger than, say, 30 light years in diameter (15ly radius) quickly becomes unmanageable and detracts rather than adds to a gaming/fiction experience.