It forces you to whittle your categories down to ten (and sub categories). I would argue that in and of itself is a useful constraint.
It's basically the same as the described system except you are forced to categorize your files even more severely since every level of the hierarchy only allows two subcategories.
It must therefore be superior, right?
I've tried organizing by language, target platform etc. and all I ever found was that it did exactly as described elsewhere: a) projects did not fit nearly into one category or another and b) extra clicks were required to navigate to them. It also maps to how they are organized on GitHub and various package repos, which invariably give you a single searchable list.
Adopting modern and quirky organisation systems are, IME, frequently just premature optimisation, and most data in massive amounts such as photos are best organized by organic means, e.g. photos are best organized by date.
I use SimpleNote a lot for JD content and put the category in the title of each note. I type a piece of the JD number in the search box and it instantly filters down to relevant notes. Sort by title sorts by topic.
The 03.65 like naming can indeed be switched out for something with words, but I believe the best of both worlds is to make the words "unix-like", i.e. small, and explanatory.
For instance *~* 10 main directories (code, doc, vid, etc) with *~* 10 subdirectories (note, tv, movie, etc) is nice to try to fit your data into, but if one of the subdirectories has only 8 things, it's not the end of the world. This tends to work extremely well for "longer term" storage (a drive mounted beside your OS for data when 'finalized' or 'semi-finalized') but the mess of OS and everyday files isn't as appropriate for it.
He does seem to address this at least somewhat[0], but the justification is so flimsy it's hardly worth addressing. In essence, he doesn't like alphabetical ordering because the index can change when something new is added. He would prefer new folders to be inserted at the end of the list. He is evidently unaware that folders can be sorted by creation date.
[0] https://johnnydecimal.com/10-19-concepts/11-core/11.02-areas...