I too noticed that duplicate issue after using SuperDuper. So I asked Dave Nanian, the developer, if he had insight. His reply:
"The reason you see multiple items, after using SuperDuper!, is because you're creating new copies of the applications (on the backup). Since the paths to these applications are different, LaunchServices puts them in again."
And, if you are not already bored to tears, a bit of background:
In OS X, Launch Services maintains a central data structure, the Launch Services database, in which it records all of the pertinent information about applications and the kinds of document files and URLs they are capable of opening. Whenever a new application becomes known to the system (such as when the user drags it from an installation disk into the Applications folder), the application is registered with Launch Services, which copies the needed information about the application into its database. Launch Services can then use this information to determine the preferred application for opening a given document file or URL.
Well, at least that's the way I understand it.