Meanwhile, integrating Touch ID on the Magic Mouse and Magic Trackpad would be complex due to the need for secure wireless transmitting authentication.
That wouldn't really be an issue. Touch ID currently works by programming the fingerprint into the chip dedicated to the Touch ID system. When another app wants ID confirmation, it asks the Touch ID system "is this person X?" and Touch ID simply responds with "yes" or "no."
Touch ID on a wireless mouse could be the same. The communication between the mouse and the computer wouldn't need to be secure, because the only things being passed would be "is this person X?" and either "yes" or "no." The actual fingerprint ID would only need to exist on the mouse and could be sequestered (as it is in the iPhone now) so that no other software has access to it.