I am thinking that if gameplay starts at 0,0,0
Then “known” space would expand from there. Patrolled sectors may span 1000 radius from center of marker. The next closest system may be centered at 4000, 0 , 3000. To go from start to next closest sector you could fly staight to it over a time period, or hyperspace in a few seconds.
This sound reasonable? Any other suggestions? Thanks
Sounds like that old game, what’s its name… Solar Winds - only that game is in 2D. Works pretty well there. It’s a mix between action and adventure. Excellent game, really. Try getting hold of it if it’s legal or google it if you need inspiration.
I dont think that distance is important. Its rather distance / speed relation. The real question is to ask yourself what is 1 unit and how fast does ship travel? My suggestion is :
try to simulate real distances - for example, Sun - Earth distance is 1 AU (astronomical unit - 150 milions km). First system from Sun is Alpha Centaury - order of magnitude 2-3 light years ( that will be around 10’13 km). So I would divide all distances with some great number to obtain my distances
a) from nearest stars it will be, say 10’13 km / 10’8 = 10,000 units;
b) from planet to planet around 10’9 km / 10’8 = 10 units …
and so on. Then you know what speed should be. Modern spacecrafts travel at 30 km/s, but this is a game 
so let say they go 100,00 km /s, or in our units:
c) 10000km/s = 10000 / 10’8 km/s = 10’-4 units/s = 0.0001 units /s . For one hour player should traveled 0.0001*3600 = 0.36 units. Too small, but i just want to give an example here.
hope it all helps.
cheers!