First off let me say I am on W98SE.
I created and image of the Content.IE5 folder Properties and as you will see in the images below it contained 202KB-61 Files and 4 Folders. Also you will see and image(poor quality) of Winspy showing the index.dat files on my PC.
I then ran CCleaner and rebooted and retook the same images and you will notice the difference. The 32.3KB-6 Files and 4 Folders is the default after a deletion, whether I use CCleaner or delete the Content.IE5 folder in DOS. You will notice a couple of index.dat files left in the Winspy but these are just harmless MS ones.
I also used the following in DOS to be sure the Index.dat files were empty with no residual junk left over:
CD\WINDOWS\TEMPOR~1\CONTENT.IE5
EDIT / INDEX.DAT
There were none present but the two mentioned above.
From all of this it seems that CCleaner is for sure removing the contents of the Content.IE5 folder.