Not all apps that are uninstalled leave empty folders on the C:\Program Files area. Some apps, during uninstallation would say that not all of its components can be deleted. That's when they are most likely to leave empty folders on C:\Program Files folder. You can of course install programs on other locations that may be easier to locate.
But you have to say that a number of uninstalled apps would leave useless folders on locations like C:\Program Files , C:/Users/<username>/AppData and C:/ProgramData.
I think they better issue this as a new improvement for CCleaner in future updates.
Also, I would like to comment that they should make registry cleaning a bit deeper to remove errors further. I have detected some useless registry keys in the HKEY/LOCAL_MACHINE/SOFTWARE and HKEY/CURRENT_USER/Software areas that weren't detected or removed by CCleaner.