One benefit is that it can expand the Yugioh universe in new and creative ways. Fanfiction often explores different scenarios, relationships between characters that might not be fully explored in the official story.
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.
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.
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.
Archive of Our Own (AO3) is also a great source. It has a well - organized tagging system, so you can quickly find Yugioh fanfictions that match your interests. For example, if you like stories with a particular pairing of characters, you can search using the relevant tags.
Perhaps in this fanfiction, the Shadow Realm from Yugioh has some sort of connection to the Tailed Beasts in Naruto. The characters could be on a quest to seal the Shadow Realm and prevent it from corrupting the Tailed Beasts. This would involve the Yugioh characters using their card - based magic and the Naruto characters using their chakra - based powers in a coordinated effort. Maybe the Millennium Items play a role in controlling or understanding the power of the Tailed Beasts.
Another option for the main characters could be Kaiba from Yugioh. His pride and determination would make for an interesting dynamic when faced with the neglect from the Naruto world. And from Naruto, Sasuke could be involved. He might initially see the Yugioh characters as a distraction from his own goals, but later on, things could change.
One feature is the crossovers between the two universes. In these fanfictions, characters from Naruto might find themselves in the Yu - Gi - Oh world or vice versa. And the use of bijuu decks in duels is a central aspect. These decks often have unique strategies based on the nature of the bijuu, like using the Nine - Tails' power for a really strong attack or the Shukaku's sand - based defenses in the Yu - Gi - Oh card game rules.