The issue is by using the Z-axis in certain situations you get a huge advantage--parking the Sova on top of a HW, the Orkulus on top of a star base, flying over or under mine fields, etc., etc.
Using the Z-axis to counter this is impractical...if you move a starbase up or down it can still be out-positioned, you can't spread enough mines to cover effectively and there's impractical to really place significant defenses on top of a planet because they take away from the need in the rest of the gravity well.
Having a Z-axis in the game is very helpful and prevents some awkward collision issues with the models but having access to a Z-axis movement control is something we can do without. A lot of things in the game seem to really have not been designed with this in mind.