Have you actually scanned with CCleaner, at the moment the latest version has no implementation for scanning for Duplicate files. That's why it is deemed as one of the safest cleaners. Programs do install duplicates in different folders and deleting them can cause problems.
Don't worry, it won't show duplicate files. To some it might be over the top but at the end of each day I run CCleaner before shutting down and in 2 years has never caused a problem.