No he wasn't.
He struggled against Youzhny, but Nadal always does. Same as Federer always struggles against Canas. It's just a player who gives him trouble.
Nadal struggled against Soderling because of the rain. Without the rain delays it would have been a straight-sets defeat. Nadal had match points in the 3rd set. So it would have been an easy victory without the on-off-on-off-on-off events.
Djokovic is the number 5 in the world, and on this years events only, the number 3 in the world. It was always going to be a close match . Prior to Wimbledon, they've played 3 times this year - twice on hard-court(1 each both in straight sets), and once on clay (Nadal in straight). All the tournaments have been big ones (Nadal beat Djokovic in the Indian Wells final; Djokoic beat Nadal in the Miami QF; Nadal beat Djokovic in the FO Semis). If Djokovic played Federer it would have been close too. You can take it as a guarantee that 3 of the semi-finalists at the US will be Federer, Nadal and Djokovic.
Remember Nadal is a dominant number 2. With the results he has, he would have been number 1 for the entire period that Hewitt was number 1 (and also for all of the musical chair period). It's just Federer is a dominant number 1, so despite Nadal's results being good enough for number 1 for a lot of the early 00's, it's not good enough now. Both of them are so dominant, that if after Wimbledon, they don't play again this year, they'll still probably be number 1 and 2 in the world at years end (No matter the result of Wimbledon final Nadal is ahead of Federer this year). At worst they can be 2nd and 3rd.