If you have it done by a vet that knows what they are doing then their discomfort will be minimal. At just a few days old, the nerves in the tail, feet and ears have not yet begun to fully function and the sensation they will not be as bad as some imagine. Some of ours have never even woken up from their puppy nap while having it done.
Mom may want to lick at the tails, my female never even acted like she noticed. Just make sure that she doesn't seem overly zealous in her efforts and that the site doesn't look irritated. It will scab overe quickly and should be fine.
