Completely false. Djokovic defeated Federer in 3 at the AO 2008 and the AO 2011, while he defeated Nadal in 3 at RG once and at the AO once. In other words, Novak has defeated Federer and Nadal, respectively, twice in Slams in 3 sets. Federer may be a better server but Nadal is a better returner, he breaks more return games than Federer both on hard and clay. In the same way that for Djokovic it is easier to break Nadal's serve than Federer's serve, for Nadal it is easier to break Djokovic's serve than for Federer (the AO 2019 final was an exception).
Also, if it were "harder to shut out Federer like that for Djokovic" we would expect Djokovic to have a better H2H against Federer than agaisnt Nadal. Yet, we get to observe how Nadal leads the H2H over Djokovic in Slams 9-6 (including 2-1 at the US Open), while Federer has a losing H2H against Djokovic in Slams. Federer doesn't lead the H2H over Djokovic in any single Slam.