No, it was annoying and I was never able to find shit. Since they were categorized by taxonomy you'd need to be a fucking biologist to know which folder contains which monsters, and since it was just filesystem path and not data in the file you couldn't even use it for something. With a flat folder you can just type the letters in explorer and enter/shell and tabtabtab and you have it. A few hundred files is not a big deal for a filesystem and collisions aren't a problem, it doesn't matter how the files are called, there's an extra attribute for monster's name ingame.