Considering that he's throwing those deep balls to guys like Wes Welker, Julian Edelman, and Brandon Lloyd, I'd be shocked if his percentage was very good.
Nobody was complaining about his deep ball when any combination of Moss/Gaffney/Stallworth were on the team. Just watch: if Dobson turns out to be any good, Brady's completion percentage on deep balls will mysteriously get a lot better.
Maybe he has lost accuracy on his deep ball. It's possible, I guess, but we really just don't know at this point, because he doesn't have anyone to throw deep to.
Also, PFF is a terrible source.