Agassi had said that were it not for a "freak" like Nadal, Federer would have won a couple calendar Grand Slams and equal Rod Laver's record. So yeah, maybe Nadal did hurt Fed's career a little. But what about the reverse?
I would like to look at what one does to the other. This is based on nothing more than my own observation, backed by some facts, but it's still mainly one guy's opinion.
First let's look at Federer. It does appear that he could have won at least two calendar Slams without Nadal, because both times, it was Nadal who beat him in the finals of the French Open.
Not only that, he could have equaled Sampras's record of six consecutive year end number 1. In his worst year, 2008, he still made it to three GS finals and won one. Had Nadal not been in the picture, it might be hard for any other to beat that performance. His total tally of Slams might be twenty by now.
So overall, Fed got hurt a little, but even with Nadal in the picture, he still broke tons of records, made lots of money, and quite a few people is willing to bestow the GOAT title on him.
On the other hand, Nadal could have ended five consecutive year end number 1 without Federer. Every year that he was ranked number 2 behind federer, Nadal swept the clay court tournies, RG, was excellent on grass, and was not shabby at all in the hard court events. For another player to beat him to the number 1 ranking, that player must either win two Slams, or one Slam and gains more points than Nadal at other events.
Looking at the field, no one outside of Federer or Nadal had reached two Slam finals in a year from 2005 to now, and since Nadal had already dominated the clay court events, the chance of any other player dominating hard court and indoor events as thoroughly as Nadal did the clay court events, based on performance of the rest of the field, would be slim. Murray could have had one good year, but I'd still pick nadal to end the year number 1.
And Nadal could have won two or three Wimbledons.
So it's obvious Nadal was hurt the most by not being able to reach number 1 for a long time trying. Otherwise, if a player ends five consecutive years as number 1, he belongs to the pantheon of the really great. Along the way, he would have enjoyed the many perks that came with the number one ranking.
Instead, Nadal held the record for being number two the longest, being constantly questioned about his longevity, which, had he already finished five years at number one, would be moot point.
The conclusion: It appears Federer hurts Nadal's career much more than Nadal hurts Federer's career, but ironically, a guy that affects your career this much is a guy you can beat more often than not.