"The question arises, if many of those anatomical structures are not really necessary, why do we have them in the first place?"

Lots of people would ask same thing about the abundance of fat cells in the human body.

Do the few brain cells somehow "know" what is necessary?

That damaged brain seems to me like city which has been nuked. Why didn't the "people" riot? Or is it a city bombed and it did have massive riots and those riots are a part of the present damage?

The brainless civil servant has a low IQ, so it seems very likely that at least some of the loss was necessary for average intelligence. And I doubt that any loss of brain matter will make anyone smarter. It's a scientific fact that damaging certain portions of the brain could make some people "more manageable" or "less excitable", but I'm not aware of any removal that has actually improved the mind.

Likewise with more than 6 billion human brains on this planet, it doesn't seem likely that the removal of any of the +6 billion brains will improve the human mind.