From what I understand, they are in the master file, but for some reason, they don't spawn. I've sunk hundreds upon hundreds of hours into Skyrim since Nov 11th, and the only transformed werewolf I've seen in the wild was
It's kind of disappointing, because it makes Lycanthropy feel like a
deal, minus the two aforementioned execptions.
It's probably worth pointing out that I don't fast travel, so it's not like I bounce around to cities or dungeons only, and expected to see a Werewolf there, I spend a great deal of time on and off the roads.