Well, I cringe at the thought that people will see them for the first time in numerical order. But you are right that the father revelation will surprise no one, no matter what order they're watched in, simply because it's become so cliched that even non-Star Wars fans know that Darth Vader is Luke's father. It's something that's parodied and revived all over the place, so it's not the same kind of original shock that it was 25 years ago.

Whoops, sorry. You were talking about how Vader knew. So, yeah, you have a point, but I think it's one of those things that doesn't have to be spelled out for us. But I seriously doubt, that in any version, people will be confused as to how Vader knows. It's spelled out enough already.

1. The crawl... "obsessed with finding young Skywalker."
2. "The Rebels are there... and I'm sure Skywalker is with them."
3. "We have a new enemy: Luke Skywalker." or, if you must...
4. "I am certain that the young Rebel that destroyed the Death Star is the offspring of Anakin Skywalker."

So by the time Vader does reveal who he is, the audience really isn't left wondering, "How did he know that?"