If this Jolteon uses Electric-Defuse on, for example, ThundurusEX, and in the next turn the opponent changes ThundurusEX for another EX pokemon, would that pokemon be able to attack?
Yes, the new Defending Pokémon would be able to attack. The reason behind this is that when a Pokémon goes to the Bench, all Special Conditions and effects on it are nullified.