And what if a large files gets infected?
I don't think it's a good idea... if you have specific files that you think are safe and you don't want them to get tested, you can put them into the list of FileSystem Shield exclusions. But setting a general size limit, without linking it to a special location, is dangerous - it might prevent scanning of files you didn't actually want to include.
(Besides, I am not sure if the size and the scan time is connected here - my guess would be that the files in question are some kind of archives, and their scanning may take longer even if they were small.)