One possible reason could be a traumatic event. Maybe he witnessed something so horrible that it made him shut down his emotions to protect himself. For example, if he saw all his friends killed in front of him, it could be too much for him to bear and he just numbs himself.
There are several potential reasons. It could be a result of a psychological experiment gone wrong. Some fanfictions like to play with the idea of Naruto being a test subject, and this could lead to his emotions being numbed. Another aspect could be related to his role as a leader. In some fanfictions, to be a strong and effective leader, he might believe he has to hide his emotions. Additionally, it could be a reaction to the expectations of others. If everyone expects him to be a fearless hero all the time, he might start to suppress his true emotions to meet those expectations.
She could have had a traumatic past. Maybe she witnessed a horrible event that made her shut down her emotions to protect herself.
In fanfiction, there could be a new type of chakra - based technology. Scientists in the Naruto world, with malicious intent, use this technology on Naruto. They strip away his emotions by interfering with his chakra network, which is closely related to his mental state. As a result, he becomes an obedient weapon for their dark purposes.
One possible reason could be for a mission. Maybe in the fanfiction, there is a mission that requires Naruto to go undercover as a girl. This would allow him to access certain places or information that would be otherwise unavailable to him as a boy. Another reason might be for self - discovery. Naruto could be curious about what it's like to be a girl and decides to explore that side of himself in the fictional world.
Perhaps a dark power corrupts him. In the fanfiction, there could be some sort of dark chakra or evil entity that latches onto Naruto. This entity could slowly eat away at his emotions, starting with his heart, making him gradually lose his ability to feel empathy and turn heartless.
Perhaps he makes a deal with a powerful entity. In order to gain some extraordinary power to save the village or his friends, he has to sacrifice his voice. It could also be due to a side - effect of some new jutsu he tries to master. The jutsu could be so powerful that it takes away his ability to speak as a trade - off for the new abilities it gives him.
She might have realized how much Naruto has sacrificed for her and their friends. His selfless acts could have made her feel that she needs to protect him in return.
Perhaps she was raised in an environment where showing emotions was not acceptable or was even punished. If she grew up in a strict family or a very repressive society, she might have learned to suppress her emotions so much that she became seemingly emotionless over time.
Perhaps the discovery of some dark secrets about the ninja world could make him ruthless. For example, if he finds out that the village leaders have been using him or his friends for some immoral purposes all along. This new knowledge could shatter his world view and make him question all his previous beliefs, leading him to become a more ruthless individual who is out to change or even destroy the existing order.
Maybe he discovers some dark secrets in the Blood Prison. These secrets could be about the corruption of the ninja world or some hidden evils related to powerful people. This new knowledge might make him lose faith in the system he once believed in, leading to his transformation into a darker version of himself.