I had the same issue, come to find out that reaper doesn't like having the Helix native vst3 file in it's stock location.
There is a readme file in the documents installed with reaper that tell you to install any VST's to user/Username/appdata/roaming/reaper/plugins.
I did the same as you and reinstalled reaper, reinstalled native, and nothing worked even if I added the right folder to the reaper vst path.
Once I copied the Native VST file to the above folder. It got recognized and works perfect now.