Some antivirus applications may prevent Carbon Copy Cloner from reading certain files, mounting or unmounting disk image files, or, in general, degrade the performance of your backup. In some cases, antivirus applications can even affect the modification date of files that CCC has copied, which will cause CCC to recopy those files every time as if they have substantively changed. In another case, we have seen such software create massive cache files on the startup disk during a backup, so much so that the startup disk became full.
CCC always examines the files on the destination to determine if they already match those on the source. If you have a volume that is virtually identical to your source, CCC will copy only the items that are different between the two volumes.
Some applications won't work when transferred to a new disk or when run on a different Mac. This has nothing to do with whether or how CCC backs up your data, it comes down to the serialization requirements imposed by the software vendor (e.g. their anti-piracy strategy). Some applications will work just fine, some will simply require that you re-enter your serial number, while other applications will require a reinstallation from the original install media or online reactivation via the vendor's website.
Yes and no, it really depends. Performance will be affected during the clone (especially the first one) as CCC reads the entire source volume and writes to the destination volume. If your work is "disk bound" -- that is your applications are reading or writing to either the source or destination, then you'll notice a performance hit. If you're just reading email or writing a Pages document, then you probably won't notice the performance hit.
Carbon Copy Cloner logs its activity to a file located at /Library/Logs/CCC.log. You can use this log to verify the productivity of your scheduled tasks. To view CCC's log file, choose "CCC Log" from the Window menu. Beta versions of CCC will produce more output than non-beta versions. Additionally, you can manually enable debug logging by choosing "Enable Debug Output" from the Help menu.