If you run CCleaner without making any config changes, it will remove your pinned documents from the quick list in Excel, Word, etc., along with the other Recent docs. At least this is the case with my setup (Win7/Office 2007). I realize that you can avoid this by using exclusions of different kinds in CCleaner Options, but in my mind that shouldn't be necessary. If an element is pinned, it's because I made a conscious decision to keep it, and it doesn't make sense for CCleaner to remove it, at least without an explicit confirmation.
It is a good suggestion, but it may be tricky to programmatically find out how to tell if a shortcut is pinned or not.
I'm trying to understand if/how this information is stored, either in the shourtcut file itself or in Office configuration files, but nothing found so far in MS documentation and forums.