They could both be tired of the expectations placed on them in the village. Naruto is always expected to be the hero, and Hinata is expected to be a proper clan member. Running away gives them the freedom to be themselves and build a life on their own terms.
Love. Naruto may finally realize his true feelings for Hinata and want to be away from the chaos of the village to be with her in peace.
Hinata might be in danger, and Naruto, being the heroic type, decides to run away with her to protect her. Maybe there's a powerful enemy targeting Hinata specifically, and Naruto thinks the best way to keep her safe is to take her away from the village.
Maybe he's running away from the pressure in the village. There are always high expectations on him, and he might feel suffocated and need some time alone to figure things out.
From a security perspective, Konoha would be weaker. Naruto is a very powerful ninja, and Hinata is no slouch either. Their skills and abilities would be missed. Enemies might see this as an opportunity to attack Konoha. Also, Naruto has been a symbol of hope for the village. His departure could lead to a decrease in morale among the villagers. They might start to feel less secure and more pessimistic about the future.
They might run away because they want to explore the wizarding world on their own terms. Without the restrictions of Hogwarts or the watchful eyes of the Ministry of Magic.
Maybe for love. They might have fallen deeply in love and want to be away from the prying eyes of the wizarding world.
Perhaps in the fanfiction, Ciel discovers some dark secrets about the Phantomhive family or the underworld they are associated with that are so disturbing that he decides to run away. He wants to distance himself from all the evil and corruption, hoping to find a place where he can be free from all the burdens that come with his family name.
Maybe he feels misunderstood by his family. In many Naruto stories, his family situation can be complex. If he's 'godlike', he might have powers that his family doesn't understand or fears, leading him to run away to avoid conflict or being treated differently.
Another reason could be related to a prophecy or a hidden mission. They might have learned about a prophecy that required them to leave Konoha in order to fulfill it. This could involve finding a powerful artifact or learning a special technique that could only be achieved by being away from the village. Their departure would then be a sacrifice for the greater good of not just Konoha, but the entire ninja world.
They might choose to run away secretly because they want to be alone together. They are in love, and the hustle and bustle of Hogwarts life doesn't give them enough privacy. So, they run away to a quiet place where they can enjoy each other's company without any interruptions.
Perhaps Naruto feels that Kushina is being overprotective. He wants to prove his independence and go on his own adventures without her constant supervision, so he decides to run away.
One possible reason could be that Naruto might be afraid of the intense training Jiraiya has in store for him. Jiraiya is known for his strict and grueling training methods, and Naruto, being young and sometimes impatient, might just want to escape that for a while.