As PeterT said, the Kobo Utilities plugin has a function to find and remove any orphaned cover images. But, there shouldn't be many. Deleting a book through the device has always removed the images for me. The same goes when using calibre to remove a book. I'm not sure what happens if you delete a book from the file system, but I am fairly sure the cover images will be removed when the device detects this has happened.
When do you think the cover images are not being removed?
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