It could be that she doesn't trust the people around her completely. Maybe she has a past experience where someone used her intelligence against her. So, she decides to keep it a secret until she's sure she can trust those around her with this part of herself. In the fanfiction, perhaps she's had a run - in with a false friend who tried to steal her ideas related to magic, so she's more cautious now.
One possible reason could be that in the fanfiction, her parents might have made a sacrifice that left her alone, and she resents them for not being there for her. Maybe she feels abandoned and that has led to her hatred.
One possible reason could be a curse that was placed on her secretly. Maybe an enemy from her past, someone she thought was defeated, managed to put a slow - acting curse on her. Another reason might be a side - effect of some powerful magic she used to save someone or solve a difficult problem. For example, if she used time - traveling magic in a wrong way, it could have negative consequences on her health.
She could use a magic - suppressing charm. This charm would make it so that her natural magical aura is hidden from other wizards and even from magical detection devices. For example, if a wizard were to pass by her with a magical detection spell active, they wouldn't sense her magic. Another way is by only using very basic and small - scale magic when absolutely necessary. Like if she needs to light a candle in a power outage, she might use a very tiny and discreet fire - making spell that looks almost like a normal match being lit.
One reason could be that the author lost interest. Maybe they started with a great idea of a female Harry Potter but then got distracted by other things in life or new fanfiction ideas. Another reason might be that they received negative feedback which demotivated them from continuing.
Well, Naruto has always been there for Sasuke in the original story. In fanfiction, Fem Sasuke might secretly like Naruto because she sees his loyalty. He's constantly trying to bring Sasuke back to the right path. This loyalty could translate into a deeper affection in the fan - created stories.
One reason could be for protection. If there's a new dark force emerging, Harry might hide his child to keep it safe from being targeted.
Well, a lot of these fanfictions focus on the idea of Harry being underestimated by others because of his 'chosen one' status. But in reality, he's secretly very smart. So, themes of proving himself to others are common. Additionally, some explore his smartness in terms of understanding the political side of the wizarding world, like how magic laws are made and how to change them for the better.
It could be due to his upbringing. If he had a different environment or set of experiences growing up, it might have affected his cognitive development. For example, if he was constantly distracted or not encouraged to study and learn, he could end up being less smart. He might have been more interested in playing around rather than reading books or practicing magic, which are important for developing magical intelligence in the wizarding world.
One reason could be fear of social ostracism. Hobbits are a traditional society, and a male hobbit being pregnant is something unheard of, so Bilbo might be afraid of being shunned by his community.
One possible reason could be that Hermione realizes she has feelings for Ron and wants to avoid any confusion or mixed signals with Harry. She might think that by pushing Harry away, she can focus on her true feelings for Ron.