I was thinking about the registry and it can make some sort of sense. Just at a glance you'd be able to know from where the shuttlecraft originated. Of course there's also the matter that the craft's origin is also on the hull be it U.S.S. Whatever or a starbase.
Yeah... the idea of SB 11 /41 (or whatever)... that would be the 41st small craft assigned to Starbase 11 ... makes perfect sense.
And a Starbase would have a LOT of assigned craft. That we saw a shuttle with a low number is mainly, most likely, because that was the craft reserved for senior personnel (like, say, a Commodore).