G E Predator said:
The reason he asks (in the 2004 DVD version) "how is that possible?" is because he is still a bit astounded that he has a son even though he knew Padme had died.

Yeah, Anakin was always quite daft, so I guess it makes sense to change Vader's character a bit to follow suite.

"How is this possible? The man who pulled the wool over the eyes of the galaxy for all those years, and manipulated me and lied to me personally countless times told me she had died, so there is no doubt she had really died. Since galactic technology is pretty low tech and primitive, there is absolutely no way the baby could have been saved by medical means... oh man! I am so confused! Ooooh, my head hurts! Ouch, gotta stop trying to force myself to think so hard! Gotta go meditate on this."