I use a sloppy meld of Zettelkasten and PARA for this very reason. I used to get nervous about the subject ontology, and the link-to-anywhere aspect of ZK's tag

I use a sloppy meld of Zettelkasten and PARA for this very reason. I used to get nervous about the subject ontology, and the link-to-anywhere aspect of ZK's tags fixed that for me. Plus having a unique ZK tag on every file means I can move subdirectories around to suit what I'm working on at the moment without any links breaking.