Yep.
Once the GUI is open, there are two ways to do this. One is on the interface itself, and the "how-to" may vary depending on what skin you use. (See the picture. Where the hand-shaped cursor is, a balloon tip is present that says something like "click this button to scan inside zipped archives, that wasn't captured in the screenshot.)
The other way is when using the menu button to start a scan, four setting options come up: select scan area, select scan sensitivity, scan archive files (that's the one) then start scan.