Freezing the cupcakes will cause the cookie to soften during the thawing process because of condensation. So the cookie won't be crunchy, but I don't think that will ruin the cupcake.
I bake all my cupcakes 1-2 days before they are needed. I store them in clam shell containers. They stay very moist in those containers. Plus you can stack the containers 3 deep, so transport is easy.