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.
Definitely Hogwarts students. They'd come during their free time or on trips to Hogsmeade. They'd be eager to try Harry's special magical treats.
Hermione would probably be a regular. She'd come to the cafe to study while enjoying a warm cup of Butterbeer latte. She might even bring some books from the Hogwarts library to read there.
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.
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.
Other ninjas would be likely customers. They need things like kunai, shuriken, and ninja wire which Naruto could sell in his store.
I bet the regular customers would include some of Harry's old Hogwarts friends. Maybe Ron would stop by for a butterbeer and a chat. Hermione might come to relax after a long day of research. And of course, the Weasley twins would probably be there often, looking for new business ideas or just to have some fun.
Voldemort would still be a very likely villain. He would see the Hulk as a threat or a tool to be used for his own evil purposes. He might try to control the Hulk's mind or use dark magic to make the Hulk do his bidding.
Another possibility is Winky. She is also a house - elf. Winky was a bit of a tragic character in the original books. In the fanfiction, if Harry were to summon a servant, her meek and somewhat lost nature might make for an interesting addition to Harry's side, and she could be summoned to help Harry with various tasks.
Harry Potter himself could interact with Sophie from Huntik. Harry is used to facing great challenges and having a strong sense of justice. Sophie, with her connection to the Titans, could find common ground with Harry in their fight against evil. They could learn from each other's worlds and work together to overcome a powerful dark force that threatens both universes.
Definitely Harry Potter himself. He has faced so many dark and dangerous things already, so he'd be able to handle zombies. Hermione would also be a likely survivor. Her vast knowledge of magic and quick thinking would serve her well. And Neville Longbottom. He has shown great courage and has a deep understanding of Herbology, which could be useful in creating defenses or finding antidotes.