From Aleh Cherp:
Moreover, each reference file usually relates to more than one topic and thus cannot be placed in a specific folder.
This is how I use tags and folders. It’s mostly all folders with some short term use of tags. Folders get a bad wrap, but they provide a dense relational information with little fuss. Not to mention, it makes it pretty easy to change a relationship for a lot of files by just changing the folder structure.