Whose to say the name Skywalker isn't any more common than, say, Williams or Smith or Chin? I'm sure Vader wouldn't read too many applicant's papers until after they've proven themself worthy of being in his special squadrons.
Another thing to consider... Other last names around the galaxy we know of aren't really "similar" to Luke's last name style... For instance:
Now, Skywalkers name is kind of like "Shoemaker" here on Earth... You hear Shoemaker, and you know it's an English name immediately. Skywalker, Darklighter, etc... They seem to be a "native" style of name for Tatooine residents possibly.
If that's the case, the likelihood of it being a common name is slimmed down some. It certainly seems like a Tatooine kinda thing to me then. And at the very least, if Vader heard the name Skywalker, who blew up the death star, and who Vader himself said "the force is strong with this one", then there's some simple deduction that it's a force sensetive skywalker...
Tack onto that Obi-Wan sacrificing himself so these 3 young rebels and their droids could escape... And the whole "glance" over at Luke... Could Vader have put all this together? Hell, maybe Obi-Wan was even thinking of Luke at the time (Seems he might have been) and Vader could sense/read that from him... Maybe Obi WANTED Vader to find out about Luke... Let him know there's someone out there who can turn the tide.