avast doesn't just say the folder/files can't be scanned but it also gives you the reason, password protected archive, etc. However you would need to expand the column width to se all the information in some of the columns.
See
http://forum.avast.com/index.php?topic=35347.msg297170#msg297170 this topic for more information on why files can't be scanned.
Files that can't be scanned are just that, not an indication they are suspicious/infected, just unable to be scanned.Thorough is also by its design very thorough (it scans all files) and perhaps a little overkill for routine use, were a Standard scan without archives should be adequate. Archive (zip, rar, etc.) files are by their nature are inert, you need to extract the files and then you have to run them to be a threat. Long before that happens avast's Standard Shield should have scanned them and before an executable is run that is scanned.
I have only ever done a Through Scan with Archives once shortly after installation just to ensure a clean start state, but with XP for example avast will do a boot-time scan after installation if you select it, this I believe will be quicker and reasonably effective. Like everything in life things are a compromise.