Well, a major theme is perseverance in love. Sakura's unwavering love for Sasuke despite his coldness or absence is often depicted. It shows how love can endure through difficult times. Another is the theme of self - discovery. As they interact more and get closer, both Sasuke and Sakura discover new aspects of themselves. For example, Sasuke might discover a more gentle side of himself through his relationship with Sakura, and Sakura might discover newfound confidence in herself as a ninja and as a woman in love.
One common theme is the power of forgiveness. Given Sasuke's actions in the original story, Sakura often has to forgive him in fanfics for their relationship to progress. Also, the theme of family is present. They might be seen as creating a new family together, or Sasuke coming to terms with the idea of being part of Sakura's family. Additionally, the idea of second chances is quite prevalent. It gives them an opportunity to rewrite their relationship story.
Love and redemption are common themes. Sasuke has made many mistakes in the past, and in fanfics, his relationship with Sakura often serves as a path to his redemption. Another theme is growth. Both Sasuke and Sakura grow as individuals, and their relationship evolves as they do. For example, Sakura might grow in her medical ninjutsu skills while Sasuke grows in his understanding of emotions.