Not zero, but an only insignificant residual because zero is hard to achieve in real life. Also Pripyat has some illegal inhabitants.

(I don't think debugged software is a commonly used term, so no need to discuss the meaning)

Edit: Genuine question: Would native speakers call Detroit depopulated? The shrinkage seems to be about the same ratio.

Does detroit contain zero troits?

I don't speak French, but I think that Detroit contains one big troit (strait), hence the city's name.

But that's certainly less troits than bones in a deboned fish!

Does desaturated mean a color with zero saturation?

If decaffeinated coffee had half the caffeine of regular coffee it would most certainly not be called that. Same with deboned fish.

The expectation using those terms is that only a negligible amount remains if any at all.