I use properties to represent a taxonomy classification for category, topic, and group. Using nested folders is much too restrictive since a note can only exist in a single folder, so maps, tags, and properties are much better and more flexible for representing classification and other hierarchical organization structures.

Categories

I have many interests in my PKM system: Music, Photos, Travel, Genealogy, Health, Writing, Reading, and Blog.

I classify them with a category property. And I have a category page for each of them with a category menu (like a category map).

Topics

Within a category, I have multiple topics and each has a topic page with a corresponding menu for navigation (like a topic map).

Groups

Within a topic, I sometimes have groups that I create for collections of related pages. And for these, I have a group page as a menu for navigation (like a group map).