Co2 reaction is highly, highly concentration-dependent. Rodent euthanasia ideally starts around 20% which makes them cranky and sleepy, they go to sleep, then concentration is upped to around 80% and they die very quickly. Yes, they feel bad when they go to sleep, but it is a mild bad and it's all over quickly. Rodent euthanasia horror stories are about getting the concentration wrong, not the co2 itself.

Nitrogen - as long as the flow is strong enough to remove exhaled co2 - won't make anyone cranky, but it takes longer, and the longer it takes the higher the risk of something going wrong with the setup. So, tradeoffs.