Hi Jørn, and welcome to the forum the second time around.
Sorry we missed your question the first time. I can only speak about Foxit Reader, as I have it installed, but as outlined in the new Piriform Documents, you shouldn't have any problems, unless you store important documents in temp files, or want to retain certain History items etc..
From the CCleaner Documents:
QUOTE
If an application is simply listed in the Applications, Internet, Multimedia, Utilities, or Windows sections with no details, the cleaning process will typically clear out document history (MRUs), visited URLs, and temporary files for that application.
There's a link to the new Piriform Documents site in my signature.
Hope that helps.