I agree with your decision to place important objects on a particular y plane. Freelancer did this very well while still submersing the player within an exhilarating 3-dimensional environment. A couple things surface in my mind that you may wish to watch out for during development:
1) Obvious: Avoid any mentality that "If everything's going to be at y=0.0 I won't store that y value in an effort to save space" as if you ever do decide to have objects placed in space arbitrarily you will be kicking yourself.
2) Not-so-obvious: I will only assume that you will be using this editor to also place space stations, patrols, and squadrons of ships. Assuming this is the case, I would like to refer back to point a. Ensure that in your editor you have the ability to place objects on more than just the x-z planes. It will become quickly apparent to anyone playing your game that everything is flattened on to one plane if for every planet, each space station is aligned perfectly vertically.
One suggestion to implement y-editing simply is to design your editor with x-z-editing in mind while having a side-pane that displays the object in question projected on to the y-plane from the side. Then merely add the functionality to drag the object up and down.
Good luck.
