Is there a way to send a thank you note to an employee at Barnes and Noble?

You aren't going to get in trouble. She won't get in trouble. I would also suggest writing a letter. It would actually do the opposite and make her look good.

There may also be a link to a survey at the bottom of your receipt. It seems as if most stores do that now.

That is very nice that you want to point out something good about an employee. Most people only say something when they want to bitch about an employee. Little things like that can mean a lot to people.