While I 've never tried to build a 3D star map, I've considered creating a color coded 'depth guide', using ROYGBIV where red is closest to map view, and violet is furthest away. The hexes themselves have lines colored for the appropriate depth. Even if most of your systems are within the same 'red' zone, systems further away have varying colors to denote depth from the front plane of the map. Although as stated, I've never tried this (never been interested star maps anyway), it does seem to be able to be used for depth. (But then all the different color hexes could make the map complicated to read.)