When you miss something, you're not referring to the original experience, but to a memory of an experience. Memories being mental artifacts, it's perfectly feasible to miss an imagined experience. Hence the current wave of nostalgia for the Roman empire.
Like I literally missed out on that time period, like how you could miss a class or meeting.
You're reading the title wrong. He means "I wish I hadn't missed out on the '90s-00s internet," that is, that he had been around to experience it.
I read miss here as "failed to be on time for", not as "long for". They specifically say "I wish I was around when [...]"