The main objective?

You lose if you don't have anything left. Usually it's better to resign before that, though.

terraform units don't count as units, I think fleas don't count too.

quote: Is it when you lose every building and constructor or is the death of commander enough?

Usually it is "exterminate everything that belongs to enemy".

Once you reach a certain level of superiority in unit cost compared to your enemy, all their units will be rendered always-visible, so you can mop them up without hassle.

quote: terraform units don't count as units, I think fleas don't count too.

Fleas and dirtbags do count. Units that don't count are either terraform, or are "free" units such as:
- commander and carrier drones
- teleport beacons
- wolverine mines

ZK used to be called CA (Complete Annihilation).

That's one of the things that differentiates ZK from other TA-mods(BA).