I too removed and replaced them by hand for many years. Winders are not cheap so this may be the only option one has. I do know that no matter how careful I was I was still risking distorting the spring. I also know that I distorted more than a few.
I’ve known many clock smiths who also wind by hand and say they never distorted a spring. When they make this claim I have three canned questions that I ask them.
First question: Have you ever encountered a coned mainspring? (of course they had seen many).
Second question: What do you think caused the distortion?
Third: How do you know the spring was distorted before you removed it?
(got to have fun sometime) 
I would agree that if you are very careful then you will probably be okay much of the time but if you have a winder then why not be sure?
Fred…if you don’t have the sleeves for your winder you can make them very easily from copper or pvc pipe fittings.
Enjoy,
Bob