Well, the one thing about statistics is that the numbers can be shocking but the details more illuminating. Federer is 4+ years more into the tour, that means at least 16 more slams played and usually in the ¼s or further, so at least another 50 5 set matches more to go. So the best time to compare the 5th set statistics is really when all of them have retired. Nadal/Djokovic have 4 years to catch up to those numbers. That's IF they play as long as Federer.
What's more interesting is the accusation of PED usage by Nadal and even Djokovic! The endurance shown by Nadal is astounding! I believe in the 2009 AO, Nadal played 3 or 4 5 set matches in a row, including a 5+ hours marathon against Verdasco. That he came out and played super in the 5th against Federer is impressive.
I believe the BBC had a documentary about how EPO usage could go undetected by WADA's tests. However, there is no proof and it's just not substantiable. Also remember Nadal came in as a teenager, winning the FO at 19. The drop in form isn't surprising, but an inevitability, just like Federer's (although not as pronounced). He's 29 and past his peak years.
Finally I have to put a question mark on the 2005 5 set victory by Nalbandian in Shanghai. Federer just came back from 6 week lay off due to an ankle injury and simply ran out of steam. He really shouldn't have played Shanghai, but with the rest of the top 8 out, he played, and almost won.