I don't think it's creepy to use the Wayback Machine, but whether I would comment on something I found that way would depend partly on content and partly on whether there was any explanation of why the original site was gone. In this case you have to go on content, since there's no explanation, except that it almost certainly wasn't a server crash, no longer being able to afford web hosting, or the like: either the author or the site admin decided to take them down.
So, for example, if these were personal essays I would hesitate--maybe he had an unpleasant conversation and decided he doesn't want to talk about that aspect of his life or past right now.
If the essays are political, maybe he's no longer sure he agrees with what he wrote. (A message saying "Hey, really cool essay, I really like how you explained what's wrong with Purple People Eating" might not go over well if the writer has since become a Purple People Eater.") One of my favorite authors, Ursula Le Guin, wrote "The trouble with print is it never changes its mind," in the context of a topic where she had changed her mind, and the opinions she no longer held were being quoted approvingly. Her previous ideas and opinions are still out there, of course, and the best she could do is note that she has thought about the topic and feels differently (or did at the point that the bit I'm quoting was published).
On the other hand, if several writers' essays have disappeared, I'd be more inclined to think it was the site owner's decision, not this writer's, and hence more likely to write to him about it.