Sure. Thor and Hercules have clashed multiple times in different comic series. Their fights often stem from differences in power, ideology, or the circumstances of the story.
In a kratos vs naruto fanfic battle, Naruto might have a chance if he uses his strategic thinking. He could use his shadow clones to surround Kratos and then attack from all sides. But Kratos is no pushover. His experience in combat is vast. He has fought against opponents with all kinds of powers. If he manages to break through Naruto's clones and get to the real Naruto, it could be over. However, Naruto also has his sage mode which gives him enhanced strength and perception. So it's a very tough call.
One idea could be a battle in a neutral dimension. Kratos, with his brute strength and god - slaying weapons, faces Naruto's ninjutsu and his ability to summon powerful creatures. Another idea is that they are forced to team up against a common enemy that threatens both their worlds. They start off clashing due to their different fighting styles and beliefs but gradually learn to work together.
Well, it really depends on how the fanfiction is written. If the writer decides to give Percy some new powers or boost his existing ones, he could stand a chance against Kratos. However, Kratos is a force to be reckoned with. He's faced the most terrifying foes in his own universe. Percy is used to fighting monsters in the world of Greek mythology, but Kratos has fought gods on their own turf. So generally, Kratos has more of an advantage.