What doesn't get cloned to new hard drive in Super Duper?
When you select the SuperDuper script / copy mode, you can change the scripts, that SuperDuper will run during the copy process.



As you can see, a couple of files are omitted:


So the temporary and cache files, etc. may have taken quite some space on your old disk. Some other possible reasons could be:


SuperDuper omits OSX swap files (/private/var/vm), which can become quite large
The spotlight index is rebuilt after cloning a drive. Depending on your system, the spotlight index may become quite large as well over time.
SuperDuper does a permission repair before cloning. Maybe some space was liberated on your old drive during that process.
As Richard suggested, SuperDuper does not clone the hidden rescue partition. But this should not be more than ca. 1GB