One reason could be to seek greater power. Maybe they feel that Konoha no longer offers the training or resources they need to reach their full potential. So they decide to leave and explore other places where they can become stronger.
Another reason might be that Naruto is seeking a greater purpose. In the fanfiction, his 'godlike' state could make him realize that there are threats out there that he can't face while being tied to Konoha. He may leave to protect the world on a larger scale, believing that he can be more effective away from the village.
At first, it might be a bit awkward as they are used to being in a group in Konoha. But as they face challenges together, like fighting off bandits or surviving in harsh environments, they would start to depend on each other more. This would lead to a deeper friendship. Sakura might start to see Naruto not just as the goofy kid she knew but as a reliable partner, and Naruto would see Sakura as more than just a friend who has a crush on Sasuke. Their relationship would evolve into a more equal and mutual respect - based one.
She might leave to find herself. In Konoha, she has always been defined by her relationships with Naruto and Sasuke. Leaving gives her the chance to figure out who she is on her own terms, away from the expectations of her friends and the village.
One reason could be to seek a new life away from the constraints of Konoha. Maybe they feel that they can't fully grow or explore their potential within the village. Another reason might be to protect Konoha in their own way. They could believe that leaving and dealing with threats from the outside would keep the village safer.
She might be shocked at first. Sakura has always known Naruto as someone who is very attached to Konoha. If his leaving is because of her, she could feel guilty. She might try to stop him, asking him why he's doing this and telling him that he doesn't have to go.
It would be a huge blow to Konoha. Naruto is a hero in the village, and his departure would leave a big leadership void. The villagers would also lose a great source of inspiration. Hinata is from a respected clan, and her leaving would also have an impact on the clan's standing in the village. Morale among the ninjas might drop as they see two important figures leave.
Well, it would be a big loss for Konoha. Naruto is a powerful ninja, and his absence would mean one less strong fighter to defend the village. Ino, too, has her unique skills in mind - related jutsu and communication. Their departure might also lower the morale of other ninja, especially those who were friends with them or looked up to them.
They could leave because of a prophecy. Some ancient prophecy might state that they need to leave Konoha to fulfill a greater destiny elsewhere. So they trust in this prophecy and leave their home.
Maybe they leave to find a better way to protect Konoha. They might think that by exploring the outside world, they can gain new knowledge and powers that will be useful for their village in the long run.