You can sort your plugins into custom “folders”, have a look at the context menu. Though the usage is quite a bit messy (also lacking drag’n’drop). You can create those folders also in the favourites section.
ps. I also do not understand, why there is a separate favourites system a.k.a. using stars. Why not simply a permanent, not deletable folder “favourites”? Benefit: Plugins only appear once, drag’n’drop etc. much more easy to implement.
Yeah, that seems cumbersome. It would be much easier to organize outside of Renoise and just have it display your directory structure. I got spoiled with that feature in Ableton/Reaper when I used them.