If I have my camera plugged in via the USB would CCleaner scan and clean the cameras memory i.e. pics that have been perviiously deleted but are still held in the memory?
No, CCleaner is not a file recovery program it only deletes junk/temporary files,
it will does not "scan" for junk files, it looks in specific locations for them,
a flash drive is not a default location for a program so it will not be affected.
If you want to try, Recuva http://www.recuva.com/ (made by Pirform as well, like CCleaner), you may be able to recover some deleted files from the flash drive.