Whilst Emilia may be less popular, there is at one in most years at DD's school and, as there is at least one Amelia in each year as well as various Amelies, they are bundled up together essentially so known as firstname & surname. The Emilys don't seem to get caught up in this (but I think there are only two in the school).
This might not bother you, it might not bother your DD but, remember, it won't just be school but Uni and likely the workplace too.