There could be health risks for Naruto himself. Constantly manipulating his own blood might put a strain on his body. It could lead to anemia if he overuses the ability, or disrupt his normal blood circulation. Also, if his control slips, he could accidentally harm himself in the process of using the blood - controlling ability in combat or other situations.
One possible consequence could be that Naruto is ostracized by some in the ninja world. Since controlling blood is a rather strange and perhaps 'creepy' ability to some, they might view him with suspicion or fear. This could lead to him having to prove himself more often in battles and interactions.
One consequence could be that it disrupts the natural balance. If Naruto isn't careful, his weather control might cause floods in some areas or droughts in others. For example, if he overuses his power to create rain, it could lead to excessive flooding.
There could also be environmental consequences. If Naruto isn't fully in control of his flood - controlling ability, he might accidentally cause damage to the local ecosystem. For example, he could disrupt the natural flow of rivers and flood areas that are important habitats for animals and plants.
One consequence could be that his friends start to fear or distrust him. After all, mind control is a very invasive power. They might worry that he could use it against them at any time.
One possible consequence could be a change in Naruto's power level. If Hinata can control the seal, she might be able to regulate the flow of power from it, which could either enhance or limit Naruto's abilities.
Physically, he might gain new powers or abilities as mentioned before. But there could also be negative effects. His body could reject the foreign blood, leading to internal pain and weakness.
One consequence could be moral. They would have to deal with the ethics of controlling the dead. Are they disturbing the natural order? This could cause a rift between them and some of their friends and allies who might not agree with such a practice.
A common plotline could be Naruto using his electricity control to upgrade his Rasengan. He might create an 'Electric Rasengan' that is more powerful and has different properties than the original. This could be used to defeat stronger opponents in the story.
His reputation in the ninja world could be damaged. If Padme spreads false information or reveals his secrets, other ninja might view Naruto differently. They could see him as a liability or a threat. This could lead to him being isolated in the ninja community, and he might have to fight harder to prove himself again.
Perhaps in this fanfiction, Naruto is in a situation where he has no other source of sustenance. He could be trapped in a desolate place with no food or water, and the blood becomes a last - resort option for survival. This would be a very dark and extreme take on the character, as it goes against his usual values.
One possible consequence is that he could lose the trust of his friends. If everyone believes he is responsible for something his sister did, his friends might start to distance themselves from him.