Ninjas, of course! They would come to relax after a long day of training or missions. Also, fans of the ninja world from within the story would be there. Maybe even some of the village leaders would stop by to show support for the local business.
Some of the older villagers who have watched Naruto grow up would be regulars. They would come to support his business and also to reminisce about the old days. And don't forget the jonin who are always on the lookout for a good meal. They would appreciate Naruto's hard work and the unique atmosphere of his restaurant.
I think magical creatures would also be customers. Maybe house - elves would be sent to pick up treats for their wizarding families. Hippogriffs might be lured by some special bird - shaped pastries. And even centaurs, if they were feeling a bit more adventurous, could come to the edge of the Forbidden Forest where the bakery might be located to get some goodies.
Her old Hogwarts friends would be very likely customers. They would come to support her new business and also to relive their old memories together. Hermione would probably come often to discuss books and new spells while having a drink.
Mostly wizards and witches, of course. They would be the main clientele as they are the ones who can fully appreciate the magical elements of the restaurant. Students from Hogwarts during Hogsmeade weekends or holidays would also flock there.
Other ninjas would be likely customers. They need things like kunai, shuriken, and ninja wire which Naruto could sell in his store.
Another possible antagonist could be a rogue ninja from Hailbel's past. This ninja could have a vendetta against her family or something she did in the past. When he discovers that Hailbel is with Naruto, he decides to take them both on. He might have some unique and dangerous techniques that Naruto and Hailbel have to figure out how to counter.
I think Gaara could be an ally. Gaara has control over sand and is very powerful. He and Naruto have a mutual respect for each other. Additionally, Jiraiya. Jiraiya was Naruto's mentor and has a vast knowledge of different jutsu and combat techniques that could be used against Omega Shenron.
Iruka sensei might also be involved. He has always been like a father figure to Naruto. He could give Naruto the confidence he needs and maybe even help him plan the location for the proposal, perhaps a place that has sentimental value for both Naruto and Hinata related to Naruto's early days at the academy.
Sasuke would be a likely survivor. His combat skills and intelligence would serve him well in a post - apocalyptic world. He could quickly assess threats and use his Sharingan to detect any hidden dangers, like approaching zombies or other hostile survivors.
Kabuto could be a likely villain. He's very intelligent and has a thirst for power. He could use his knowledge of jutsu and his ability to manipulate others to try and steal The Flash's speed force. He might think that by combining it with his own powers and ninja techniques, he could become invincible.