You need to learn something about statistics.
The clay has more "observations" hence the validity of saying "Nadal is better than Federer on Clay" is clear.
However, based on 3 observations on hardcourt it really means nothing. To put this into perspective.
Say France vs Germany has played 3 times in past decade. France won 2 out of 3. Is this a clear indication that France is CLEARLY better? Now consider that France and Germany has played 12 times. And France wins 8 times, and Germany 4 times. Then you can say that France is the better team.
You wouldn't be saying that if you never saw Rafa/Federer play indoors. The hardcourt h2h wouldn't strike you as being any closer than the clay h2h if you had no knowledge of their indoor meetings. You would be seeing their hardcourt results not unlike their clay meetings.
Nadal won 2009 Australian Open 7-5 3-6 7-6(3) 3-6 6-2 no different to 2006 Roland Garros 1-6 6-1 6-4 7-6(4) or 2007 Roland Garros 6-3 4-6 6-3 6-4 (federer 1 of 17 breakpoint conversion rate).
Nadal won 2004 ATP Masters Miami 6-3 6-3 (federer 0 of 0 breakpoints converted), no different to 2008 Roland Garros 6-1 6-3 6-0.
Fact is, while many people point to the 2009 Australian Open as a 'choke', even Federer's many losses to Rafa on clay were extremely close and the result of mental shortcomings more than physical. It was never about the surface. Yet throw in the indoor results and suddenly Federer has a form of tennis he can dominate 3-0, excellent breakpoint conversion rate included.