it is possible... i was just playing a multi star map and an enemy fleet came into my stars grav well (which was fortified with 4 starbases)
anyway, they jumped smack bang into the cross-firing arc of two fully upgraded SB's... who werent firing...
i couldnt figure it out... i told both of them to fire manually... and their missiles fires but not their Lasers or Beams... and i couldnt figure out why...
then i zoomed in and realised the enemy fleet was WAY above the usual equator combat line... thing... hence why the SB's werent firing. The SC were giving the enemy fleet a hard time, but they generally missed my first line of defense... i was like... BUMMER!
anyway, so yeah, Z-axis does exist... but making the game fully 3-D would require a MAJOR overhaul of some basic gameplay elements, which im not so sure would be a plus.
all i want in that respect is that certain ships fly around and 'duck and weave' around like they are actually trying to NOT get hit while in combat. i know there is a mod, but having it as standard would be nice... other than that i dont think 3D is necessary, as it would just clutter things up