I think that there are two distinct ways to describe the relationship that Bruno and Shmuel share. The first is in a literal sense. Boyne uses the friendship between the two boys to show that while the Holocaust transformed so much of the world around human beings, there were some elements that remained unchanged. Kids have to find friends. While Gretel is busy being indoctrinated in her Nazi propaganda, Bruno still feels bad that he left his friends behind in moving to "Out- With." His need to build the tire swing and to engage on an adventure is representative of how while the Nazis changed so much in the world, one element that could not be touched was that childhood carries with it its own universalities. This extends to Shmuel, also. While the Nazis sought to destroy so much, they could not remove the need for Shmuel to find a friend, to seek another companion. Even if this individual lived on the "other side of the fence," Shmuel's need to find a friend and revel in the association made was something that even Hitler could not remove. The universal truth of children needing friends is one way to describe Bruno and Shmuel.
Another way to describe the friendship of both boys would be to examine its thematic significance. In the world of the Holocaust, where what had value was deemed insignificant, such as human life, hopes, and dreams, the friendship between the boys embodies the idea that there can be resistance in the name of universal ideals even in the darkest of situations. When studying the Holocaust, there is a natural tendency to accept survival as the only means of being in the world. The horror of the Holocaust can enable the individual studying it to say, "If I were there, I would have done the same thing" in reference to the cruelty, desensitizing to human suffering, and the sense of "internal aloneness" that dominates the period. However, the friendship between both boys is a reminder that individuals, even in the darkest of times, can stand up for that which is right and embody it. Consider the Bruno is really scared when he crosses the fence and walks with Shmuel in the hopes of finding his father. He wants to leave his friend and go back, but he does not because of the promise he made to his friend. When being ushered inside the gas chamber, with the unspeakable fear of the world crushing down upon them, Bruno asserts that Shmuel is his "best friend for life." While Bruno might not see himself as a resistance fighter in the Holocaust, his friendship with Shmuel, the sacrifices it entails, and the empathy evident because of it shows how there can be embodying universal maxims of human solidarity even in the darkest of times. Survival might not be the only metric by which to examine human actions. The ability to transform what is into what can or should be is another way to describe the friendship between both boys.