Strikecraft move in the Z-axis ALL THE TIME. Turrets can swivel to engage targets above/below them. Removing the Z-axis completely wouldn't really fix the problem, and would bring a whole slew of new ones. I suggest you check the thread 'Attacks from Above'. It has an interesting debate concerning the Z-axis.
I think that Sins obviously WAS designed with the Z-axis capable. The Orkulus can already move around the Z-axis. The Argonev and Transcencia, being static, cannot. However, increasing the rates at which they can turn (swivel) would likely help with this.
Additionally, ships, and especially strikecraft, NEED THE Z-AXIS for movement. Why? Quite simply, if there was no Z-axis, then there wouldn't be Sins of a Solar Empire. It would be 'Fly around 2D Plane and kill Planets of a Solar Empire'. Think about it. No Z-axis, no SC. While ships aren't as limited in that factor, you still need Z-axis. Otherwise, how will you have your fleets of ships operate properly. If you look through screens of the gameplay, then you'll note Z-axis variations are quite common, whether it's in the position of orbital defenses, Starbases, asteroids, logistics structures & ship factories, and in ship formations.
However, the employment of the Z-axis is actually not well known. Also, ComradeYakov, please do not say that Sins obviously was or was not designed to allow something that you probably don't know for a fact. It is my OPINION that Sins was designed for accomodation of the Z-axis. I do think that it is rather obvious that it was designed for Z-axis operations; however I'm not going to try and force this upon someone as a fact.
I am not saying you are attempting to force this upon everyone. Also, there is the fact that the OP asked that this be fixed, as if it was a bug. Z-axis movement is not a bug. It is quite possibly a feature. Also, while I agree that static emplacements would need to have some tweaking, I highly doubt that the changes that would be implemented would require a complete redesign.
To the OP- You should elaborate on what you mean. Was it that anti-structure cruisers were above/below an SB and were firing on it? If this is the case, than the SB wouldn't have been able to engage anyway; Ogrov/Solanus cruisers outrange SBs.