This just occurred to me as a possible solution for you, KillMeNow. Try reskinning the Pharos (or whatever the nav bouy is called) using textures that are pure green (RGB value 0,255,0) except around the edges of the polygons, where you should put thin lines coloured at RBG value 0,254,0.
Pure green is transparent in FS2, which means the background (stars, nebulae, planets, interstellar grapefruit, whatever) show through, so your reskinned nav bouy would look only like a computer generated icon on the HUD. As long as you keep the "no-collide" flag in the table entry, you won't have any problems with collisions.