The thing you have to realize, is that if they did make it "true" 3D, who would play that?
I mean sure, it's realistic (and i'd love to see it). But now, rather than rotating your map around to get a better viewing angle, etc....anything can go anywhere. As it stands now (if you had 3D available), you could hide an entire fleet underneath a star and nobody would know a thing....well, other than the player-icons that show through objects).
All i'm saying, is that sure it's a cool thing we'd like to see, but i don't think it would be very good to put it in, as it were. It would just make things more complicated, regardless of how frigging awesome it would be. I'll just stick to using my "`" key for the Z-axis, as it suits it's purpose 