Depends on the outlook. There's a short actual harm, but they're usually sedated for that. However, the act of spaying/neutering reduces the number of unwanted pets born which reduces the net suffering of pets. Additionally, the act makes the pets more docile and therefore able to enjoy their circumstance.
If left untreated, animals might suffer slightly for it because they'd have all the disadvantages without being able to breed. This includes increased aggression.
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