I’m not really sure what to recommend you besides very basic things like reinstalling vorpX and checking for potential background programs that may interfere. Literally never heard of such an issue before. It’s definitely not something caused by you using a WMR headset.
If I understand you correctly and the actual issue is that you can’t use the mouse in the menu, that’s not really a problem though. You can also use the menu with the cursor keys + enter or alternatively an X-box gamepad.
In regard to No Man’s Sky please be aware that stereo 3D-support had to be disabled after the NMS 2.0 update last year, hence the game is not listed as a supported game anymore. You should also see a message about that whenever you start the game.