So this is now possible – sort of – in Cubase 8. I’ve just made a new plugin ‘collection’, as Steinberg calls it, and I’m sorting the plugins how I want, and I can have the same plugin listed in more than one folder, which means I can have both vendor folders and also FX type folders.
Only small downside is that it looks like I have to manually add new plugins to my collection. But this is a very useful feature, so it might tempt you into upgrading.