It would be better if you just add a balloon tray icon instead of a notification window after the scan completes. This way, there will be less interference will what the user is doing. The user can then decide what action to take after the scan has completed.
Title says it all. I prefer the scan to run even after you press the 'Minimize' or 'Close' button. You can add a notification window after the scan has finished. Many antivirus and anti-spyware products can scan while in the system tray. I see no viable reason why SUPERAntiSpyware left this standard feature.