Nadal would have more trouble against himself than most players with one-handed backhands. It's not a 1 vs 2-handed thing. Extreme topspin gives most backhands trouble. Nadal gives Murray, Tsonga, Roddick, Monfils, and many other players huge problems on their backhand wings. On the flip size, Gasquet, Almagro, Wawrinka, Kohly, Youzhny, and even Federer, handle it fairly well. Nadal's backhand is a weakness. A vast majority of players have much better forehands than backhands. A backhand weakness does not appear just because Nadal breaks it down.
I've said it a 1000 times, Federer's trouble with Nadal isn't so much his backhand. He handles that wing just fine. His problem is Nadal's quickness and court coverage. Federer is forced to play very aggressively with his groundstrokes (low percentage) and becomes tentative with his approaches because of Nadal's ability to pass on the run. Nadal on the other hand doesn't have to come far out of his comfort zone. If Nadal wasn't so effective with his backhand pass, Federer would dominate this matchup in my opinion. In most of Federer's losses you can pinpoint a game or a point where Nadal took control with one or more spectacular backhand passing shots. It happens almost every match.
As I've pointed out in other threads, Nadal's quickness and court coverage and passing ability are relative to many of today's slower and high bouncing courts that favor his defensive style of tennis, giving him time to reach balls that could be winners on higher speed courts, which then allows him to produce capable shots of his own. This forces the attacking player to hit either riskier lower percentage flatter shots in an attempt to go for winners, or, to change the nature of their game to rally with Nadal, and that becomes a losing proposition for almost any player other than Mr. Djokovic of 2011 and later.
Put Mr. Nadal on the faster lower bouncing surfaces like those you find indoors, or some of the faster hard courts on the US Open summer tour, and he can look almost helpless against attacking players and not only Federer.
Can there be exceptions? Sure, the margins between the top players are not huge. If one of them is having an off day or tournament, they can be beaten in conditions that would generally favor them, just as they can play exceptionally in conditions that don't favor them particularly, or combinations of those two. But these are clearly exceptions.
Nadal on clay is 12-2 vs. Federer - Federer's only 2 wins coming at Madrid and Hamburg.
Nadal on indoor hard is 0-4 vs Federer.
Nadal on grass is 1-2 vs. Federer.
Nadal on hard courts is 5-1 in favor of Nadal, but 4 of those wins were on the slower conditions of Rod Laver Arena (AO) and Miami, the exceptions being a win for Nadal in Dubai 2006 and a win for Federer in Miami 2005.
Their slam and YEC record generally reflect similarly. Mr. Nadal's most singular win in the faster US Open conditions was in 2010, where he served unusually well, and had a good draw. Prior to that, he hadn't gone beyond the semis (2) and had lost to lower ranked players. In 2011, the conditions were slower than usual. Mr. Federer won his lone Roland Garros major when Mr. Nadal lost his only match there to Robin Soderling, but Federer still has made 4 finals there, only to lose to Mr. Nadal.
They have met much more on clay, including the clay slam, because Mr. Federer is still an excellent clay court player and can go deep enough in a tournament to meet Mr. Nadal; he's just not as good there as the Clay Court King, Nadal.
They have almost no meetings in faster non-high bounce conditions other than the Indoor YEC, because Nadal has generally not been able to go deep enough in those tournaments to meet Federer, who clearly does perform well in those conditions (5 straight US Open wins and a final).
They have 4 meetings indoors, because they are forced to meet in the Year End Championships due to the round robin and top 8 players in the world format.
There is no mystery here. These conclusions are all based on the record.