Vader didn't know that Luke and Leia were his offspring because after he was beaten by the high ground his ability to sense through the force was severely diminished. He also wasn't looking for them because he thought they died along with Padme (rip). Vader only learned that Luke was his son after Boba Fett was tasked on hunting him down (Vader comics) and told Vader that Luke's name was Skywalker. Vader flipped out and almost tore the command deck apart, then he went to the Emperor who confirmed it, Luke was his son. Vader/Anakin never knew there were twins, so Vader thought that he had found the only offspring of Anakin Skywalker. When he was searching Luke's feeling on Death Star 2.0, he realised that he and the Emperor had been wrong all along, and that there was "a sister"