On my XP Pro system, I have 2 HDDs, my primary HDD with 3 partitions and my secondary HDD has just one partition, this is where my drive imaging software backups are stored (the last six backups) and also other backup files.
So I can't see how or why multiple partitions would slow the scan and it doesn't seem to do that on my XP system. What could slow scans if you haven't got much free space and or a lot of fragmentation on the HDD.
Personally - With a resident on-access antivirus like avast, the need for frequent on-demand scans is much depreciated. For the most part the on-demand scan is going to be scanning files that would be otherwise be dormant or inert. If they were active files then the on-access file system shield would be scanning them before being created, modified, opened or executed.
I used to have avast set to do a scheduled weekly Quick scan, set at a time and day that I know the computer will be on. But I have ceased this practice for some time now, based in the above.
The smart scan should be really quick as it only scan certain files I could probably complete a smart scan whilst compiling this post (slow typist). The scan is currently on 37% and it didn't hang about long on 0% and it has now completed. See image1 for the elements of my Smart Scan and image2 for the Viruses & Malware element of the overall scan (and the lack of files being scanned).
Note: I don't have lots of other elements on my Smart Scan as many of the other Tools I haven't installed, so not much in the way of what I call superfluous scans.
Whilst none of this should take anything away from the issues you are having, I just can't understand why.
If I were experiencing this, I would report it and then I would stop doing the scans as having done them once and leave them. Check back after other updates and see if the issue is still there, but when this is only happening on a limited number of systems it is going to be hard to pin down if it is a system or avast issue.