One common theme is family acceptance. Since in the original Naruto story they are not siblings, the fanfictions often focus on how they come to terms with being related. Another theme could be the change in their relationship dynamics. For example, Sakura might become more protective of Naruto or vice versa. Also, the impact on their friends and the ninja world in general is often explored, like how their new family bond affects the way others see them and interact with them.
Well, in a lot of'sakura is narutos sister fanfiction', the theme of shared secrets is quite common. They might have to keep their new relationship a secret at first for various reasons. And then there's the theme of rediscovering their past. Maybe there are memories or events from their childhood that are now re - evaluated in light of this new revelation. Additionally, the theme of loyalty within the family is also explored, as they have to stand by each other against any threats or misunderstandings that come their way.
A major theme is identity. Sakura and Naruto both have to redefine who they are in relation to each other as siblings. There's also the theme of growth. Their new relationship forces them to grow in different ways. For instance, Naruto might become more understanding of family values, and Sakura could become more confident in her role as a sister. And of course, the theme of friendship still plays a part. Their friends' reactions to this new family connection and how it affects their friendships is often a part of these fanfictions.