Did his father ever realize what happens to Bruno in The Boy in the Striped Pajamas?

Yes, Bruno's father does realize what happened to him. It takes him a while to figure it out, though. One day, Bruno goes missing all of a sudden, and despite all the soldiers at Auschwitz searching high and low for him, he's nowhere to be found. All that's left of him are some items of clothing left by the fence.
Eventually, Bruno's father puts two and two together and realizes to his horror what happened to his son. He now knows that the only rational explanation for Bruno's sudden disappearance is that he somehow ended up in the gas chambers, where he died along with countless Jewish prisoners. He doesn't know about Shmuel, of course, but he does know that Bruno's dead and, what's more, how he met his end.