A powerful dementor - like being that has been corrupted by Asgardian dark magic. This entity could be draining the life force of both wizards and Asgardians. It would be up to Thor and Harry Potter to find a way to stop it, as it poses a threat to both of their worlds.
It could be Loki. Since he has a knack for causing trouble, he might find a way to cross over to the wizarding world. He could manipulate the dark wizards and use their magic for his own devious plans. Maybe he wants to steal the Philosopher's Stone to gain immortality and use it to take over Asgard as well.
One possible plot could be that Thor somehow gets transported to the wizarding world. He might initially be confused by the magic there as it's different from his Asgardian powers. Harry Potter and his friends could be intrigued by Thor and his hammer. They might team up to fight a common enemy, perhaps a dark wizard who has somehow got hold of some Asgardian artifact and is misusing its power.
One possible plot could be that Thor ends up in the wizarding world of Harry Potter. Maybe the Bifrost malfunctions and he lands near Hogwarts. He could be mistaken for a very powerful wizard at first. Then he teams up with Harry Potter and his friends to fight against a new dark threat that is using both magic and some form of Asgardian - like power. Thor could teach the wizards about Asgardian combat and they could teach him more about the nuances of magic.
It could be a Death Eater who has somehow made a pact with a powerful force from Scorpian's world. This villain would be extremely dangerous as they'd combine the dark magic of the Harry Potter universe with the unknown and potentially deadly powers from Scorpian's realm.
Lex Luthor from Supergirl's world could be the villain. He could somehow find a way to travel to the wizarding world and team up with some dark wizards. He wants to use magic to enhance his power and take over both worlds. Supergirl and Harry Potter would have to stop his evil plans.
It could be a powerful demon from the Inuyasha universe who has somehow managed to gain the ability to absorb the power of gods. This demon would see Thor as a prime target to drain his powers and use them to conquer both the Inuyasha world and potentially other realms. The demon's dark magic and newfound god - like powers would make it a formidable foe for Thor and Inuyasha's combined forces.
Yes, there are likely some out there. Fans often create crossover fanfics that combine different universes like 'Hitman' and 'Harry Potter'. These can be really interesting as they blend the magic and mystery of 'Harry Potter' with the stealth and assassin - like nature of 'Hitman'.
Another option could be a new character created specifically for this crossover. This character could be a wizard who has studied the ninja arts and has become corrupted by power. He could start by causing chaos in the wizarding world, using his magic to mimic some of the more dangerous ninja techniques. Then, he could set his sights on the ninja world, seeing it as another source of power to be conquered. Fem Naruto and Harry Potter would have to put aside their differences and work together to stop him.
It could be a wizard who has gone mad with power and wants to control both the wizarding world and the underwater realm. He discovers a way to use dark magic to manipulate sea creatures and cause destruction in Aquaman's kingdom. He then sets his sights on Hogwarts as well, seeing it as another source of power.
Voldemort could still be the main villain in a different way. Suppose he discovers Tonks' unique connection to Harry and tries to use her as a weapon against him. He could manipulate her mind or put her in dangerous situations to force Harry to make sacrifices or bad decisions.