If you are using the AES external methods, yes, each is a separate stream and has to be configured following the guide. The smil is consumed by the player for switching purposes, has nothing to with encryption. You can generate one file then make copies, changing the name to stream names you want to encrypt. The same external script can handle many streams with the same key. Again, if you just want to add encryption, you can use the internal method with simple configuration, no key files or external scripts.