Having many moles overall is considered a risk factor for melanoma, whether or not they are atypical is what I am told. Yes, the risk may go up a bit more if you have a TON of atypical moles but still it is only a small % of risk. It is the same if you have blue eyes, fair skin, blond hair, etc.
I have ALL of these mentioned above and still all my derms tell me that the risk is higher for me than say my husband, especially since I have had melanoma, however, an average person’s risk is like 2% or something….where my risk is like 10%, so at first it scared me, but then I think, well that is still like 90% chance I don’t get another. 
Jenni