This module goes through all of your /site/assets/files/ directories and removes those that have no files in them.
http://modules.proce...ean-empty-dirs/
Pages with file/image fields require a directory, so you should expect that some of the removed directories will be re-created by these pages.
As of today, ProcessWire no longer creates directories for all pages, so this module is mostly useful to existing sites rather than future sites.
I am listing it as "alpha" just because I've only tested on my own sites. Once I get confirmation from others that it also worked well for them, I will change its status to stable. Until it is considered stable, I suggest only running it in dev/test environments (not that it does anything dangerous, but just a good practice).