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