Topic Folders
It can be quite useful to have specific folders for certain topics. For example, in my Efforts, I have topic folders for my Areas, Interests, and Projects.
This seems like a natural way to use folders to organize a set of related files together in the same folder. Of course, they can be referenced with links from notes anywhere within my PKM system.
Minimize hierarchy
It just makes it easier to know where certain topical files belong when you have topic folders. However, this requires that they must not have a deep hierarchy or they become overly complicated.
For example, in my existing vault, I initially thought it would make sense to use folders to categorize my notes. So I established category folders, and topic folders within the category, and sometimes even group folders inside the topics. This wasn't too bad in the early stages, but as the notes in my vault grew over time, it became a problem.
Maps over folders
Now I realize that maps, views, collections, tags, and properties are much better ways than folders to categorize my notes with a taxonomy for classification and hierarchical organization structure. However, sometimes while developing a map, it can be useful to use topic folders while organizing a groups of related notes.
Package folders
These can also be useful to develop packages for outputs from my efforts. For example, I might want to make a compressed zip file from a Package folder for a group of notes to be available as a download on my website for Plus subscribers.