Is the school a school for war orphans?
I hope someone who is familiar with the original story can answer this question. The reason I ask is that when the kids go to see the chairman of the board, or whoever he is, he asks the girl "What did your father do?", in the past tense. But I don't think he knew any of the kids before they showed up in his office. He seemed to just assume her father is dead.
It is an important question, because it may explain why the students are so attached to the school and many seem to think of it almost as their home. If it is true, then the boy must have known already that his own father was dead and that he was adopted by the parents he lives with.
The movie is just full of little details and hints like this. Also I love love love the response of the chairman: if this is what you want, then it is my job to find a way to do it. It is an important message of the film. That attitude is pretty rare among school administrators in the US, and I suspect even more so in Japan.