Maybe he feels betrayed. In the original story, Naruto has faced a lot of discrimination in Konoha when he was young. So in the fanfiction, it could be that some similar or new issues make him decide to hide.
One reason could be that he feels misunderstood by the villagers. Despite all he has done for Konoha, some still hold grudges or are afraid of his power. Another might be that he wants to explore the world on his own terms, away from the responsibilities and restrictions of Konoha. Maybe he also feels a sense of loneliness there, as he has lost many important people and the village constantly reminds him of those losses.
In this fanfiction, it could be that the Sith from Star Wars somehow make an alliance with the dark forces in Naruto's world. Konoha then has to rely on both their ninja skills and some newfound Star Wars - like technology or magic that has also been brought into their world. For example, lightsabers could be modified to be used by ninja, and the Force could be a new power source that some characters start to explore.
It could be that Konoha wants Naruto to use his influence to bring peace among different clans. Naruto is well - liked and respected, and his words might carry a lot of weight.
Perhaps he has hidden the full extent of his Sage Mode abilities. He might be able to stay in Sage Mode for a much longer time than he has shown so far, or have some other undisclosed powers within that mode, like the ability to sense enemies from much greater distances.
He could be hiding from Orochimaru. Orochimaru has always been interested in Naruto's power. Maybe Naruto has discovered a new power that Orochimaru wants even more desperately, so he hides behind a mask to avoid Orochimaru's detection.
Naruto might end up feeling extremely lonely. His family has always been an important part of his life. Without their support and presence, he could become depressed or start making even more reckless decisions. Also, if his family tries to search for him, they could get into danger themselves in the process, which would be an unintended consequence of his hiding.
Well, in some fanfictions, Naruto might outsmart Konoha by using his unique knowledge of the village's secrets that others don't know. For example, he could use his understanding of the old tunnels under Konoha to his advantage in a situation where he needs to escape or gain an upper hand in a conflict.
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.
It would create a sense of panic. Naruto is a very important figure in Konoha. His strength has been crucial in protecting the village. Without him, the villagers would fear attacks from other villages or threats from the Akatsuki. For instance, if the Akatsuki knew Naruto had left Konoha, they would likely see it as an opportunity to capture him more easily.