I had a similar problem which turned out to be a shortcut/symbolic link to the vst3 folder that was inside the vst3 folder.
This caused Studio One to index 10,000 plugins each time it loaded (I don’t have ten thousand plugins, it was just indexing the same ones repeatedly — up to a maximum of ten thousand times).
Deleting the shortcut sorted the problem. Not sure how it got there in the first place.
HTH.