>"nihil" means "nothing"
>"ego" is the rational part of the brain, the mediator between "id" and "superego"

Based on etymology, and it's Pokédex entry stating that it's a parasite that may or may not be sentient, I believe Nihilego's assimilation behavior is based on an instinctual desire to have personality. Nihilego has no mind of its own, but it knows it can temporary obtain one by taking over the bodies of sentient creatures.

Nihilego is an eldritch horror glass jellyfish that possesses intelligent beings in order to fill an instinctual void of intelligence in itself.