Without knowing what scan you did (all local drives, thorough, with archives, I suspect), the amount of data to be scanned, your OS, Processor and RAM, I couldn't really comment.
This, the interactive response is a limitation of the free home version, advanced automated actions are in the Pro version. When you detect the first on the pop-up check the don't show this again and select No Action, that will allow the scan to complete and at the end you get a list of files that require action.
Archive (zip, 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. Thorough is also by its design very thorough and perhaps a little overkill for routine use, were a Standard scan without archives should be adequate.
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.
