You never get away from eventually drilling down into folders; that’s inevitable with a hierarchical structure.
We are in agreement viz numbers vs letters. The advantage, as I noted, is that adding [43.12] to an email subject is less confusing or obtrusive than adding [Finances.TaxReturn2020], but the numbering scheme adds more cognitive work to recall or look up various numbers.
Using a single letter (“F”) of course is a problem if you also have an area named Food. The advantage to numbers having no association with the topic is that there is no incentive to have the Food area numbered 12 or 42, so the same lack of association that makes it more work to remember the numbers makes it easier to assign them.
One of the ways I avoid “drilling down” for frequently accessed folders is to assign a tag to the folder itself. Those “folder tags” start with an @ sign to distinguish them from other tags that I use for searching and categorizing. I can open any such tagged folder instantly through my own scripts in Alfred, and there are a very small number of them reflecting folders I need to open very frequently. Not a perfect scheme but it helps me a lot.
I totally agree about not using the “.”, and would use something else, probably a hyphen as you suggest. My file naming scheme presents a date in YYYY-MMDD format, with alternative formats of YYYY-MM or YYYY-MMDD-HHSS when needed, followed by a descriptive file name, with NO special characters. All spaces are replaced with an underscore (very useful as I do a lot with scripts and in the shell where spaces in file names is a royal pain), and of course the extension starts with a period.
I don’t rename every file this way, but pretty much anything that needs filing/archiving and most working documents will have this format, and I have my own script that can process a file name into this format, using a supplied date, or pulling a date out of the file name itself (eg if I named the file YYYY.MMDD.extension, with spaces and the date at the end and with a period in it, which is faster to type), or with the file’s creation date or content creation date. Thus it is very quick for me to select a bunch of files in Finder, fire off a KM script that renames the files, and queue them up for filing.