It’s never stupid to ask a question. My guess is that the reason you are a good student is that you are intellectually curious. It’s as honorable to be curious about yourself as it is to be interested in your studies. Since your school offers you a free service, why not take advantage of it?
One behavior does not determine a diagnosis. Many people have odd little ticks or gestures they use when under stress. We all have to learn to self-monitor for when it is socially unacceptable to indulge in them. Hand-flapping is probably a way you discharge nervous energy. In private, it works for you. You just need to learn other ways to manage anxiety when you are out.
I’m more concerned about your sadness, confusion and isolation. It may be that you are getting depressed. Or it may be that you need some help learning how to cope with stress and manage your feelings. Or both. A counselor can help you figure out what’s going on and what you need to do to have a happier life.
I wish you well.