I seriously don't think so. He'll eventually lose matches to him, especially on clay and slow hardcourts, but I don't think he'll ever have like, a 5-win lead in their H2H. IMO, it might take long, but their H2H is gonna end up in Roger's favor. Unless they only meet on clay
which I sincerely don't hope so, because that would mean Nadal would certainly lead their H2H, however that he's no good on other surfaces.