However I would like for it to be answered, so could you guide me if you have suggestion to improve my question, so I might get an answer? Is it too broad/specific, vague, ...? Any suggestion?
You're asking us to pick a hypothetical folder structure for you. This is not really a computer problem, it's simply a matter of choice (hence why you're getting votes to close as "Opinion-Based").
You seem to be aware that (some) file systems have problems with containers over a certain size. Investigate what those limits are for you target file system(s) and pick a method to separate them that suits you - alphabetical, by date, by wiki section, rotating though numbers folders, etc.
Congratulations on your badge. I'm surprised it didn't get down voted too! :-) If you hover on the downvote icon it will explain what it is used for and I think it applies to your question. Get another badge for taking the tour. Also your question has been generally answered.
The following is probably why others have not answered and may cause debate over a matter of opinion:
- If I was going to build a Wiki the folder structure would mimic the structure of the Wiki topics. I guess if you ask the next guy he will come up with something else.
- GUIDs are useful but they don't strike me as an intuitive thing to use for a Wiki.
- Several thousand files probably are no effort for any modern day file system, had you got this far then I am sure people would be able to offer solutions to a real problem - but for now your question is theory and they don't often attract real world answers.
All the best, Al