Hey...I'm playing multiplayer and in space fields I can get near 180 fps. However, the interface waypoints tank the FPS significantly. So I am in space and my FPS is 80...and I press F6 to move those yellow waypoints and arrows all around the screen and on the hud and the FPS goes to past 170. If simple arrows rendering is causing such a problem, they need optimising somehow.
One day the Devs will do many optimizations, that's for sure, but currently they focus on bringing on all those additions which hadn't been possible in earlier game developments stages. Until than Players have to live with the FPS Pains. You can try to change In-Game Graphic settings which have the most impact on performance to an eventually lower level. Settings like Texture Resolution, which is a real FPS Killer.
The way-points, yellow or white, have significant impact on FPS when they are shown on the HUD. Try using the detector less than you do and keep only one or two yellow way-points active at a time. Also weather has impact too. Rain, fog, hale thunderstorms etc work against FPS.
One thing that I do not understand is why way-points on another playfields are displayed too. Would be way better if only the way-points on the current playfield were there. There is many room for improvement in this regard. Being able to set different colors for the labels of these way-points would be very helpful too; the same as being able to filter these, upon category, to select this that you want see.
When you place a bookmark you get several options for it. I believe "waypoint" causes it to show up in other playfields, so simply don't check that box.