I've been looking for an answer to this on Google, but have yet to find a reason. I think it's really fascinating that all her daughters had the first same name, and was thinking maybe it was an Austrian tradition, or related to religion somehow?
It was a Habsburg tradition, and had been since the 17th century, so it wasn't Maria Theresa's idea. It was also to show the family's and Austria's special devotion to the Virgin Mary, so you're doubly right.
source: Marie Antoinette: The Journey, by Antoina Fraser