I don't think Roger thinks it had an effect on Nadal either.
But I have no problem with him calling Nadal (or anyone else) out on their silly time wasting. If more players didn't put up with that BS he wouldn't get away with it. Plus the Umps need to do a better job of enforcing the rules. But if they don't do sqaut when Roddick calls them a "f*cking asshole" I guess I shouldn't be suprised they let Nadal abuse the time limit between points.