Marc,
The main thing to keep in mind regarding PDMW is that it operates on a "flat" file structure. In other words, any folders you may have in your vault are just for your benefit, and to keep things visually organized. They have very little effect on how PDMW stores its data. Bradley and Scott are correct; there is not a specific limit on how many files per folder, but as your vault grows in size, it will take longer to do the tree rebuilding and structure validation. That will be true regardless of your folder structure. Bottom line, you can make the folder structure as simple or as nested as you want -- whatever makes sense to you and your company.