Johnny here. The problem is "especially with something like x" because x never exists in any enterprise. Go ask your BigCorp SharePoint sysadmin for broot. The answer is no.
Regardless, the main point is that numbering directories as a mnemonic is more of an encumbrance than a help. The justification on the website, that it prevents new directories from disrupting the user's mental map, is unconvincing. There are many methods for that that don't require a team to align on a numbering system and fixed directory order - shortcuts, bookmarks, snippet managers, broot, and z, to name a few. Not all methods are available in all contexts, but at least some are.
Prepending numbers, on the other hand, forces users to, at best, waste time learning a system they might not need to use again or, at worst, bikeshed about what number to give a new directory or how to renumber if a change is needed. Users can't even skim directory names because the order is fixed and they've been robbed of the ability to sort alphabetically. The larger the team, the worse all this becomes.
They start at `01` and increment. I still remember back in 2007 at the National Australia Bank, the WinXP deployment project stored its DNS designs in folder `53`.
My theory is that people do this because the alphabet is unreliable. What was the name of that DNS designs folder? I don't remember. But it could have been any one of a bunch of things: DNS, Designs (DNS), Dynamic Name System, so on. That choice is essentially arbitrary because we have this language full of synonyms. And so how do you remember it and the dozens of other folders that you use regularly? You don't!
Numbers lock things in place. `53` will always be there. The person who created that doesn't give a hoot about `52` or `54`. They just know that their stuff is at `53`.
Adding a whole bunch of new folders that start with 'B' would have messed up the spatial placement of our `53` folder, but now that's not an issue. `53` is always exactly where it was, and muscle memory can develop.
I dunno. I haven't done the studies. I'd love to! But this is a pattern that I see over and over. To dismiss it as 'wrong' ignores the fact that people are doing this for a reason. There's something natural about it.