My general rule for when to put the JD ID in the file name itself is to do it when it will help you within whichever application you usually open the file.
So for example, when I’m viewing PDFs — say it’s my travel insurance certificate — I’d typically navigate to the folder first in my file system, then find the thing (probably 101.16.ID) and then double click to open; vs. opening Preview, the PDF application, and using the menu there to open. I just don’t do that with PDFs.
In this case having the ID in the file name is no benefit so I typically don’t bother. (Not that it would hurt. I’m just lazy.)
Whereas at work when I have Excel documents, I often go to the application first. Or it’s already open. So now I’m using the File > Recent menu or equivalent, and it’s here that I find having the IDs in the name really helps. I can scan that list of recent files, my eye leads me to the correct file based on its category or whatever, and I open it directly.
I find this scanning a list of recent files by number vs. name to be easier on my brain.
The other case where this is extremely useful is detailed in Numbers in file names: now officially endorsed.