Hmm. I just ran a couple of tests on this on 3.7 and it doesn't seem to do anything at all.
I uploaded a file into the uploads folder, clicked Scan. Nothing.
I uploaded a file via the Media menu. Shows as unattached, of course.
So I searched around online and there's absolutely no documentation that I can find, anywhere.
The only thing I found was a core Trac item where someone had optimized the scan. In the comments (here: http://core.trac.wordpress.org/ticket/10911), someone says:
"Initially this scan was designed to catch attachments where the parent post is deleted, i.e. post_parent > 0 but post doesn't exist, not orphan attachments with post_parent = 0"
So, assuming this is correct, the "Scan" button ONLY looks for attachments where the post has been deleted, not files on disk which have no post or unattached attachments or anything.
Given that WP should handle this situation anyway (by unattaching or deleting the media file when the post is removed), it's pretty much a redundant waste of time, IMHO. It would be much better if it scanned the disk for floating files. :)