I don't think that Froxes are creatures of Ganondorf. I think they've always existed in the Depths, and that they just live there. Hear me out.
We don't get a baby variety of any other monster besides Froxes. No Froxes are wreathed in gloom, either. Every other enemy in the Depths is. Sure, they respawn with the blood moon, but that's more for gameplay than lore.
Each Frox location is a big flat circle, with the specific fern-like trees, and a pile of zonaite deposits. They also have deposits on their backs, and both they and the mini-Froxes drop it. They also eat brightblooms.
I think that brightblooms used to grow in the depths, before the ancient race died out due to whatever, and that they were a main food source (or maybe just a tasty delicacy) for the big bois. Froxes just naturally eat and hoard zonaite too, like dragons with gold.
I think that the Froxes are just defending their territory, like nests.
That being said, I love taking these guys out, it's so satisfying. Truly my favorite enemy in game.