It is a bit strange that you ask for metaphor in The Boy in the Striped Pajamas because metaphor is precisely what I do not find. The handful of metaphors that I do find are of an unusual sort. They compare people to abstract ideas, and the abstract ideas may be labeled with capitalized words. For instance, when Bruno thinks about his sister Gretel, he refers to her as the Hopeless Case. In this metaphor "Hopeless Case" refers to the abstract idea that Gretel will never be anything better than what she is and that what she is is really pretty poor and in need of a great deal of improvement--but the improvement will never come. She is a Hopeless Case.
He wasn't particularly bothered if Gretel was being sent away because she was a Hopeless Case ....
Another instance of this type of metaphor comparing people to an abstract idea is his way of thinking about the other boys in the other families in his neighborhood in Berlin. The other boys are either friends or trouble. Comparing boys to trouble is a metaphor that makes an analogy between boys and the abstract idea of trouble. In this case, Bruno means that these boys can make life very difficult for him by being unkind; this is why he steers clear of them:
other boys lived in them who he played with (if they were friends) or steered clear of (if they were trouble).
there were no other houses anywhere to be seen, which meant there would be no other ... boys to play with, neither friends nor trouble.
On the other hand, there are a fair number of similes. One is rather a poetic simile in which carefully growing flowers at Out-With is compared, using the word like, to a candle in a dark castle;
flowers which grew in neat orderly sections in soil that looked as if it was tended very carefully by someone who knew that growing flowers in a place like this was something god that they could do, like putting a tiny candle of light in the corner of a huge castle on a misty moor on a dark winter's night.
Personification also occurs such as when Bruno describes Lieutenant Kotler's hair on a Saturday: "his hair flopped down over his forehead in exhaustion." Bruno gives Kotler's hair the human-like characteristic of feeling exhaustion and of flopping down in response to it. Though there are some very interesting literary techniques in the story, which, in fact, add to the humor of this unhumorous narrative, the technique of metaphor is a difficult one to find amongst them.