anti-Necropolis faction

Well, firstly, in the patch with the Knight faction, you can't create an unlimited number of them; there's a limited quantity. Secondly, the Necromancer can cast spells like madness, suggestion, blindness, or even mass slow on humans, so it's not entirely straightforward.

But does it really matter which upgrade you choose?

It's very important because the alternate upgrade is very helpful in fighting mage heroes. By activating the ability of goblin shamans, they significantly weaken the spell of the hero or unit on which this ability is activated.