One popular theme could be Hermione struggling with a magical illness that no one fully understands. Another might be her dealing with the emotional toll of being ill while still trying to keep up with her studies at Hogwarts. Also, her friends' reactions to her illness, like Harry and Ron trying to find a cure or just being there for her, are common themes.
In Hermione illness fanfiction, a prevalent theme is the role of her intelligence in dealing with the illness. She might use her vast knowledge of magic and potions to try and figure out what's wrong with her. Additionally, the theme of her relationship with her teachers during the illness can be explored. For example, how Professors McGonagall or Snape might react differently to her situation compared to other students. There could also be a theme of her facing discrimination or pity from some students due to her illness, which she would then have to overcome.
Well, a common theme in Hermione illness fanfiction is the exploration of how the wizarding world's medicine fails to immediately help her. This can lead to her seeking out alternative, often dangerous, magical remedies. There's also the theme of her isolation during her illness. Since she's so used to being in control and active, being bedridden makes her feel cut off from the world, which is an interesting angle for many fanfic writers.