I'm going to allow that some things, like photos for example, can live in their own folder apart from the Johnny Decimal data hierarchy.
(Also, it would force me to consider ... do I need 1000 files here? I've certainly been known to join related documents into a single PDF, Uber-document, if you will.)
"It’s very unlikely you will end up with a hundred categories." -the page
Exactly this will result in about 20-30 folders for most, with any real amount of documents some folders might hold 100-1000 docs.
The advise you should take from this is that forcing structure is useful. Look att large code repos for example.