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Evolution is based on time, pollution you produced (not absorbed) and spawner kills.
The reason why it depends on the situation is because suffering from arracks costs you resources (ammo and repairs) that could have been turned into science packs.
When the attacks are small and far between, they don't cost you all that much so it can be fine to leave the nests be for a bit while you focus on expanding your factory.
But if your resources are limited and/or if the attacks are big enough then it's better to quickly get rid of the nests responsible for the attacks.
Sure, killing spawners adds a chunk to the evolution factor but your goal should be to maximize your production, especially science packs, in order to grow faster than the evolution.
If you can secure oil and unlock flamethrower turrets, you have already pretty much won after all.
2. Evolution is based on pollution produced so having nests in your pollution makes no difference. Except for the pollution created by making and supplying your defences.
3. It is best to wipe them out as soon as possible. Killing the nests will increase evolution a little bit but producing the ammo or energy or oil for your turrets will make pollution that increases evolution and you are most likely going to have to clear the nests eventually anyway so better to do it sooner rather than later.