No, you don't need to disable System Restore for ANY type of scan. My anti-virus (by default) excludes the System Restore files from scans. If yours doesn't do this by default, you may need to manually tell it to not scan the "C:System Volume Information\restore" folder. I use Ad-Aware, and it works fine without turning off System Restore. I would never turn off System Restore.
Am I supposed to disable the System Restore every time I scan, for anything? Could you explain when I'm supposed to disable System Restore when scanning? Do I disable it, then immediately start running the many scans, then enable it again? It's just that my System Restore rarely makes restore points by itself (whole different problem!) and I could lose everything, possibly. The scanning takes a long time (online scan, Ad-Aware, Spybot, The Cleaner, etc.), does that matter?