In such a fanfiction, it could be due to a misunderstanding. Maybe Naruto was forced into a situation where he had to act against the Yugioh world for the sake of his own village. For example, if there was a threat to Konoha that was somehow related to the Yugioh realm and he was given no other choice but to 'betray' them.
He could be betrayed by a false friend in the DxD world who spreads lies about him. For instance, telling others that Naruto has a hidden agenda to take over their realm.
In a more complex scenario, Naruto could be influenced by an outside force. Let's say an enemy of Konoha uses mind - control or some form of manipulation on Naruto. They make him believe that the ANBU is the enemy of the village and that he needs to take them down. As he betrays the ANBU, he slowly starts to realize that he's been used, but by then he's already in too deep and has to find a way to fix the situation and regain the trust of his friends and the village.
In this fanfiction scenario, Naruto's betrayal by Akeno could be due to a misunderstanding of their goals. Maybe Akeno has been influenced by some dark forces that made her turn against Naruto. It could also be that there is some hidden information that led to this sudden change in their relationship.
In fanfiction, Naruto being betrayed by Akeno could be a very interesting plot twist. It might start with Akeno having some hidden motives or being forced by an external power to turn against Naruto. Maybe she was blackmailed into doing so. This could lead to a whole new set of adventures for Naruto as he tries to figure out why she betrayed him and also deal with the consequences of her actions.
The relationship between the Naruto universe and the Yugioh universe might be severely damaged. There could be a rift that affects not only the characters directly involved but also the overall balance between the two fictional worlds. Maybe there would be crossovers of characters trying to fix the situation or make things worse.
A more complex idea would be a fanfiction where the concepts of chakra and duel energy are somehow related. The characters from both universes try to understand and combine these energy sources. For instance, Sasuke could use his sharingan to analyze the patterns in Yugioh duels and gain an edge in battles.
One possible plot could be that in a crossover world, the Yugioh characters are somehow transported to the Naruto universe. However, the Naruto characters neglect them, thinking they are just strange intruders. The Yugioh characters then have to find a way to get back home while dealing with the indifference of the Naruto world.
Yes, there are quite a few. You can start by looking on fanfiction websites like FanFiction.net or Archive of Our Own. Just search for 'godlike naruto yugioh' and you'll likely find some interesting reads. Some might combine Naruto's powerful ninja abilities with the strategic card game elements of Yu - Gi - Oh in really creative ways.