CSS/JS aggregation, huge number of files
As noted in the post you found: 


  They will be deleted automatically 30 days (or whatever your
  drupal_stale_file_threshold variable is set to) after they were
  created via drupal_clear_css_cache() and drupal_clear_js_cache().


If you are going to have many thousands of users worrying about file system performance at this stage is likely getting ahead of yourself. Depending on your hosting setup you are more likely to run into other kinds of performance issues (PHP, database, fewer non-file caches, etc) before the file system becomes the bottleneck. You may indeed need to solve that problem eventually but it is unlikely to be the first challenge you need to overcome.