One common theme is the growth of their relationship. They start as friends or comrades and then develop deeper feelings. Another theme could be them facing challenges together and relying on each other.
In 'naruto breeds sakura fanfiction', a frequent theme is the exploration of their unfulfilled potential in the original series. Authors often write about how they could have been a great couple if things had been different. There's also the theme of their shared dreams and how they support each other in achieving them. For instance, if Sakura has a medical - related dream, Naruto could be shown as her biggest supporter, and this kind of relationship - building is a common theme in such fanfictions.