1.The relationship between Bruno and Gretel was consistent with that between most preteens and teenagers and their younger siblings. Gretel felt more mature and better about herself when she could put Bruno down for being "stupid" because he was "only nine." She was that between age, not quite a child, but not yet a young adult. A very difficult time. Bruno's defense was typical. Classifying her as an "hopeless case" gave him a shield against her barbs. I believe the one dimensional aspect of the children is intentional. We don't need them fully fleshed out. It is only their part in the "fable" that is relevant. (B're rabbit was one dimensional also... grin) That is why our knowledge of them is limited.
2. I believe Gretel is not in the League of young Girls because of her father's position. There is a lot of opportunity for over hearing sensitive conversations that a child might innocently repeat to her father's disadvantage.
3.Bruno has many reasons to feel a chill in the house at "out with." There are many underlying currents in the house. His mother does not approve of her husband dragging his family, especially the children, along in the interest of his ambitions. The view of the camp and the people outside his window, even though he dose not understand it. The whole place is steeped in bad vibrations. Lt.Kotler's angst, Pavel's fall from doctor to kitchen help and waiter. All of it is just below the surface, just beyond Bruno's grasp.
4.Bruno stared at the people in the striped pajamas because he was confused. He did not understand, but he was questioning their differences or lack of them, as the story goes on. He is very naive and that curiosity and and naivety foreshadows the behavior that precipitates his fate.