In Episode II: The Samurai Called Jack, the Vadaquian Leader was requesting Aku for permission to live in the Earth oceans, as their home world had been drained of its water. The Shogun of Sorrow proceeds to reveal that it was he himself that had stripped the planet of its water and its riches for his own world's purposes. A young Vadaquian steps up and calls Aku a monster. The Vadaquian Leader silences him and begs Aku to spare the boy as he still young and immature, but Aku sent the boy to the Pit of Hate to learn respect and Aku allowed them to live in Earth's oceans in exchange of constructing a monolithic tribute in his likeness once a month and rise it from the depth of the oceans as reminder of his undisputed ruler of Earth.
After Aku's destruction in the past, all the atrocities Aku has done to their planet were undone. So, they presumably live there in harmony, free from Aku's evil.