If the point of analyzing H2H's is to determine the better player, it's important to take notice of the match-up issues and other factors (into which surfaces the matches played have divided etc) which affect only this rivalry but none other bc every match-up is different. What is clear that the match-up issues in the Federer-Nadal rivalry affect the play least indoors.
1) Half of their matches have been on clay, a surface Nadal is considered the GOAT
2) They've never met between Wimbledon and YEC/WTF, a mind-boggling statistic considering that stretch is a bout third of the tour year.
It's clear so that a random future Fedal-match will likely be on clay or slow hard, and it will be likely won by Nadal. It will do nothing in determining who is the better player, as H2H's rarely do.