I wouldn't think it would have much difference, as far as search engines are concerned. Note that some supposedly don't like it when your page is 4 or more directory levels deep, but I don't know if that's documented anywhere. Coming up with a unique name for each page may not be a good use of your time. Human users will understand your site's functional layout better when you use directories. If you currently have a directory structure, I'd just leave it as is -- I don't think you'll gain enough (if anything) to pay for the effort of converting.