See Purge of .crypted files ? or orphan resources?
On mobile the only way it is possible to delete crypted files is to uninstall the app and therefore delete anything. On desktop, you can delete the crypted files when the app is not running. If you know how to write bash (or some other scripting language), you could write a bash script to manually run when Joplin is closed, which will delete all .crypted files in the .resources folder where there is no matching file without the crypted extension