Drupal CKeditor image-upload plugins don't delete unused files
Try to check out the Fancy File Delete module. One of the things it can do based on the module page is 


  Deleting unused files from the whole install that are no longer attached to nodes &amp; the file usage table. AKA deleting all the orphaned files.


I think this would require a manual process of deletion but this may solve the issue of deleting orphaned or unused duplicate images in your site.