Since dogs have much better hearing than people, and the train whistle hurts your ears then it is a safe bet that it hurts her ears too. If it does hurt her ears then there is probably not much that you can do about it. My dog whines every time the fire company sounds it's alarm, and whenever a police car , ambulance, or firetruck goes by within a 1/4 mile of my house. Since it lasts a very short time I guess we all just have learned to live with it and he doesn't seem to have any lasting effects because of it. As far as the vet goes, maybe you should look into another one, at lest try to find one who knows the difference between spaying and neutering.