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.
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.
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.
Yes, there are likely fanfictions out there with Naruto being scared of Kakashi. Fanfiction writers often explore different character dynamics, and this could be an interesting one to play with, like perhaps in a scenario where Kakashi shows a very strict or intimidating side that Naruto hasn't seen before.
One possible reason could be his past traumas. He grew up lonely and was often shunned by the villagers. This lack of positive human contact in his early years might have made him wary of touch in fanfiction. For example, the constant glares and cold shoulders from the villagers could have made him unaccustomed to friendly or affectionate touches, leading to fear.
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It could also be related to his jinchuriki status. The Nine - Tails' chakra within him might make him feel that being touched could lead to the unleashing of that power accidentally, and he's afraid of harming others or losing control. So, to avoid any such situations, he's scared of being touched.
One reason could be Kakashi's Sharingan. It's a very powerful and somewhat spooky ability. Naruto might see it in action in a way that scares him. Maybe Kakashi uses it to subdue an enemy in a really intense way that makes Naruto realize how dangerous Kakashi can be.