For Ninomyia nailing the weapon to a horses foot (causing it pain), thus trying to hide his involvement and cause the horse to be blamed. And for Okusu feeding the horse chocolate to help help hide the accident. These two actions are very criminal and turns two people who proabaly would have not gotten jail time to a murderer and someone who would be an accomplice.
Had he called the police right after the accident, it would have easily been able to been seen as self-defense, but by hiding it it makes him much more liable to be convicted of murder, why? Becasue Ninomyia's word is all he had, Conan never proved that he was attacked, and I think there is no acutal proof that it was indeed self-defense, and as I mentioned, hiding it makes Ninomyia's case much harder to defend.
Even if Ninomyia and Okusu aren't charged for murder, they will be charged with covering it up. Animal cruelty charges may apply too, but I'm no scholar in Japanese law, so I don't know all of what they could face.