Hello,
I finally managed to get CC to clean Waterfox cache, and I thought I would share my solution with other WF users. And no, CC does not clean Waterfox cache by default, even though WF is based on FF. That used to be true, when WF shared the same profile folder as FF, but not anymore.
FF and WF have the same profile structure, so I followed the guide below (method 1), with some minor modifications :
http://www.piriform.com/docs/ccleaner/advanced-usage/ccleaner-ini-files/how-to-clean-user-data-from-non-standard-mozilla-browsers
On Windows 7 (and 10 I think) each