I think there are two major reasons why the layouts are so two dimensional:
1. To Increase the Perceived Size: One of the main "features" to this game in the marketing material is the size of the game's universe. By placing everything in a system on the same plane they need fewer items to reach the desired density of locations in the system. If they were to place the same number of locations in the system over the same x-y area but vary location on the z axis greatly from location to location the system would feel much more empty, which while probably more "realistic" would greatly change the feel of the game and probably prompt even more criticism that it's all empty than there already is (justified or not).
2. Accessibility: It's seems clear to me that a lot of effort has gone into making this game accessible to a wider audience than space games usually enjoy. The interface is streamlined and simple, the control scheme is easy and effective (and doesn't require a seperate purchase), etc. Removing the feel of easy reference (same plane, autoalign on autopilot) they remove some of the "lost" feeling that space games can give you. Don't get me wrong, I'd love it if the game lacked the autoalign (although align prior to autopilot dock makes perfect sense) and the z axis was used just as much as x and y. But this would make the game more confusing to the wider audience they seem to be after.
BTW, Starflight and Starflight2 were fantastic games. I'd love to see a freelancer style game with a universe that explorable. More specifically I'd like explorable planets where you land then get out of your ship, climb into your little moon buggy and explore the surface either to mine, search for artifacts, or collect life forms. The three hundred or so star systems that Starflight boasted wouldn't be bad either.