Yup, it often can mean discomfort. But a nose-lick can also be a way of clearing his nose. I see this more often in cats, who seem to have a wider range of smells they dislike (largely other cats), and after sniffing something of which they disapprove will lick their noses as if to say "get this stink out of my nostrils!"

Alternatively, maybe the clever scent-hound is just keeping the tool of his trade nice and moist. ;)