What is the theme of Number the Stars?

Bravery is an important theme in the story, both individual bravery and collective bravery. Over the course of the book, Annemarie matures considerably, growing into a strong, courageous person able to stand up for what she believes. At first, she's somewhat fearful, as we can well imagine. Life under Nazi occupation was hard at the best of times, but Annemarie has an additional reason to be worried on account of her friendship with a Jewish girl called Ellen. If the Nazis discover that Annemarie's family is harboring a Jew then they'll find themselves in serious danger. Yet despite this, Annemarie knows that protecting Ellen is the right thing to do, and she digs deep within herself to find the necessary courage to help Ellen and her family escape from the Nazis.
The collective bravery of the Danish people is also much in evidence throughout the story. Numerous people risk their lives to protect Jewish folk from the Nazis and help them escape. Uncle Henrik uses his fishing boat for just such a purpose. It's a hugely risky business, and he could be caught at any time, but like Annemarie, he knows it's the right thing to do and carries on regardless.