I think that one symbol in the narrative is the fence. It is the fence that divides worlds of reality. On one side of the fence, the best wine is served, dinner conversation is pleasant, and life is good. On the other side of the fence, the worst in human cruelty is evident. The fence is a symbol because it demarcates this difference i reality. At the same time, the fence is also a symbol of how this can be overcome. Bruno and Shmuel meet at the end of the fence, where it can be burrowed under and overcome. The fence and its divisions are overcome with the friendship of both boys. While they die in the process, the symbol of division is overcome.
I would also suggest that another symbol in the novel would have to be the gas chamber. It is in the gas chamber where death is evident. Yet, the symbolism of the gas chamber is that everyone in it is equal. Death is universal. At the time, Bruno and Shmuel, one German boy and one Jewish boy, are seen as the same. There is no difference in the cruelty of the gas chamber. Yet, it is within this realm where Bruno clings to Shmuel's hand and tells him that they will be "best friends for life." A symbol of destruction ends up becoming a testament to how human beings should act. In this instant, the gas chamber is a symbol of transformation.
I feel like the smoke clouds played a big part in the symbolism factor of this book. It showed that there was death in the air, moving all around, all the Non-Aryans were killed and burned. Knowing it was there but not knowing how to get rid of it.
A possible symbol could be the "striped pajamas" themselves, since they do play a big role. It is what divides the Jewish from the Germans, more specifically Bruno's family in this case. It is also, technically speaking, the reason why entire Jewish communities were being murdered off the face of the Earth.