Members of both groups are accepted to YC but then randomly selected as to who actually goes with YC or not. [1]
Of course just knowing that you have been accepted to YC (or telling others) would no doubt skew any outcome. Just like knowing you were accepted to "a Harvard" and/or telling people you were will skew how you are perceived.
That said there certainly could be a study (sans the halo effect) done of startups, as a group that applied but were rejected by YC vs. those that were accepted.
Sounds like something that mattermark could potentially take on. Or maybe priceonomics in a blog post.
[1] Then, years later, compare outcomes.