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.