We tend to use the word "choking" way too liberally anyway, and it's often when a match is close but doesn't go the desired way for us as fans. Mats Wilander, who showered Zverev with praise (and rightfully so) brought up a very good point: Zverev was actually never close to winning the match, as the last two sets ended 6-3 6-2 in Nadal's favor.
Therefore, portraying this as some big missed opportunity that Zverev blew away is disingenuous. You could even argue that as good as he played, he was marginally outplayed for 4 out of 5 sets, as I really think Nadal was the better player in the third set but Zverev's serve ultimately won it.
We need to give these kids a break. Zverev was coming up against a better conditioned, far more experienced opponent who as you said, is one of the best ever. Experience plays a huge part in these matches as little things like navigating the match on a point-to-point basis, making strategic adjustments, playing the big points a certain way, and other subtle factors all influence the result heavily, and that is why the higher rated players will more often than not come out on top in these situations.