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.
They might be afraid of how their families will react. The Weasleys have their own ideas about who Fred should be with, and Hermione's parents, while muggles, might not understand a hasty and secret marriage. Also, there could be threats from dark forces. If the wrong people find out about their union, it could put them in danger, so secrecy is key.
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.
Well, one possible plot could be that she discovers a hidden inheritance from her family that gives her new magical powers. Maybe it's an ancient magic that was long forgotten. This new power could help her in her fight against Voldemort in a way that the regular magic she had before couldn't. For example, she could have the ability to communicate with magical creatures on a deeper level and gain their assistance in battles.
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.
Yes, there are quite a few. Some fanfictions explore Harry's hidden intelligence by having him solve complex magical problems that weren't in the original books. For example, he might figure out new spells or ways to use magic more efficiently. This can add a new layer of depth to his character.
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.
To protect the person she loves. If she's in a dangerous situation, like there are still dark forces around, a secret marriage could be a way to keep her loved one safe from being targeted by the enemies.
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.