First of all, thank you for taking the time to post!
It would be great indeed! The problem with smart folders, though, is that they are not, technically speaking, folders. They are merely shortcuts to Spotlight queries, in a disguised text file.
I believe Mark Allan has posted on the ClamXav website that he would investigate the matter and consider that feature for inclusion in future releases. You might want to scan the ClamXav support forums for some more up-to-date information on the issue.