Personally, I would say keeping things simple is always a better idea in game design. Adding complexity for complexity's sake only takes away from the game itself. Complexity should only be added if it improves the game in a clear way.
Yes adding a lot of Z axis variance may be more realistic, but honestly, people think better in 2D planes when they are looking for orientation and directions. It works for dog-fighting to have z-axis variance on a scale that is proportional to ship combat, since that is one of the cores of the game - combat in space.

However, for full-system setup, the z-axis variance should probably be proportionally insignificant, as at that level of scale, you're probably more concerned about getting from point A to point B, interacting with stations and planets, etc. Making the Z-axis significant at that level of interaction adds nothing to the game. It won't make trading more in-depth, it won't make travelling between planet A and station B any more involving. They shouldn't be on the exact same plane so it's obvious, but a destination shouldn't be on the full 360 vertical range either. It'll also more likely make fleet setups easier to manage. You can still do fancy tricks by getting all over the Z axis if you want, but if you're a newcomer, it doesn't mean that you're left woefully behind by not being familiar with Z-axis positioning.

I must confess that I have a hard time getting my head around the fact that people even think that there's a problem.

But then again, that's maybe because I grew up with the Elite flight model (and it's modern incarnation in Oolite). I've said it before: controlling your space craft with pitch and roll automatically leads to an understanding of space where the "plane" between "left" and "right" is irrelevant. You orientate yourself towards your target, regardless of where that target is in the endless space around you. That's it. It doesn't matter at all at which angle towards whatever imaginary "plane" you're moving. It's irrelevant for moving in space. The only time when angles and orientation become relevant is when you line up with a docking bay. And even then the docking bay itself can be at any arbitrary orientation relative to whatever other body in the system.

Honestly, I don't understand the fuzz.

Removing one plane of movement freedom does not remove one plane of co-ordinate space. I don't understand why you're finding an issue with having yaw. You said spaceships having yaw rotation bothers you, but there's six degrees of freedom in space (three axial directions, 3 axial rotations), so I'm not sure where you're finding issue. I would think it much less natural to restrict your movement controls by removing z rotation.

In either case, if you like yaw more, or roll more, people will find a style that works for them; removing freedom arbitrarily seems to force a style onto them. For me this is one case where having more options is a good thing.