I always thought he knew that was going to happen, and he was just making sure he was dead.
Oh, you mean poking his boot into Obi-Wan's empty robes as if stunned at his disappearance? The books I've read that spell out what Vader was supposedly thinking at that moment lean in the direction of genuine wonderment....that Vader expected his lightsaber strike to cut through his former Master and physically kill him, and the sight of seeing his body completely vanish and his robes crumple to the deckplates was a big surprise.
Vader and Obi-Wan hadn't had contact with one another in 20 years so the former had no idea what the latter had learned during all that time in hiding. I'm sure Vader realized it was some sort of fantastic Force power he was unfamiliar with and the Emperor might have explained the disappearance to him at a later point (and that's making the assumption that even the Sith Master understood the event).