One possible reason could be that Kushina has a very strong and intimidating personality. In the Naruto universe, she was known to be a tough kunoichi. Naruto, who might be used to more gentle or reserved people around him, could be scared of her boldness.
One possible reason could be that Naruto has heard some spooky stories about Kushina from the past. Maybe there are tales in the village that at night, Kushina had a more intimidating presence due to her strong personality and powerful chakra. Another reason might be that Naruto has some sort of premonition or nightmare related to Kushina at night, perhaps linked to some hidden family secrets or events that he is unconsciously aware of.
In this fanfiction, Naruto's fear of Kushina at night can show his vulnerability. Despite being a strong ninja, he has this fear which makes him more human. It can also be a way to explore his relationship with his mother. His fear might lead to him trying to understand more about Kushina and their family history.
Yes, there are likely to be such fanfictions. In the Naruto series, Sakura can be quite assertive and strong - willed. Her temper and skills could potentially be a source of intimidation for Naruto in the creative interpretations of fanfiction writers.
Well, it might make Naruto more withdrawn from characters who are close to Kushina. For example, if Minato is still alive in the fanfiction, Naruto's fear of Kushina could cause him to be less open with his father as well, since Minato was Kushina's husband. He might be worried that any information he shares with Minato could get back to Kushina.
Another aspect could be that the fanfiction delves into how Kushina's presence affects Naruto's relationships with others. For instance, his relationship with Sasuke could be different. With a strong maternal figure in his life, Naruto might be more stable emotionally and be able to approach Sasuke in a more understanding way, which could potentially change the whole dynamic of their rivalry and friendship.
One possible reason could be that Naruto had a traumatic experience related to thunder when he was young. Maybe he was alone during a thunderstorm and something really scary happened, like seeing a lightning strike too close for comfort. This could have left a lasting mark on his psyche, making him fear thunder in the fanfiction.
In many Naruto fanfictions, Naruto might have developed some new and unique abilities that the Kyuubi has no defense against. This could make the Kyuubi, which is used to being a dominant and feared force, feel vulnerable. For example, if Naruto has the power to nullify the Kyuubi's chakra or to manipulate it in a way that goes against the Kyuubi's will, it would be a cause for fear.
It could also be due to a misunderstanding. Perhaps there is some misinformation spread about Sasuke in the fanfiction, like false rumors that he has a hidden and malevolent plan. Naruto, being someone who values their friendship deeply, would be scared at the thought of Sasuke turning into an enemy because of these untrue stories.
One possible reason could be Kakashi's reputation as a strict and powerful teacher. Naruto might be in awe of his skills and fear making mistakes in front of him.