The Ku enemies are more annoying than they are harmful. Their fireball attacks only do a 1/2 heart of damage. Even if Link swims right into a Ku, it also will only do a 1/2 heart of damage. For the most part, it is best to just avoid Ku, but Link can defeat them with a wide variety of weapons. Link's Master Sword will defeat a Ku in two sword slashes.
In the Light World, the River Zora lived in Zora's Waterfall alongside King Zora. While there is no King Ku, the Catfish that lives at the Lake of Ill Omen does fit the criteria of an oversized Ku enemy. Much Like King Zora, the Catfish is friendly and will not harm Link.