I can offer this suggestion, I’ve been running this way for a few years now, two custom folders. I use “C:\VST 32” and “C:\VST 64” all VSTs get installed to these folders (VST3 goes to it own folder and this is okay). I separate by manufacturer (this is optional). My 32 bit folder is not in use much anymore because I’m all 64 bit today, I should probably get rid of it.
I don’t put any VSTs in the ‘Program Files’ folder (I’m on Windows) because I’ve seen too many problems caused by not having ‘permissions’ set properly.
I never need to have Cubase (or any other DAW) search for my VSTs because I know where they are and just set the proper path to my VST folders.
Hope this may help someone.