Conformal coating and micro SD card sockets
You could try loading a dummy card while coating to act as a mask for the contacts.  In my experience, SD cards themselves are quite hardy to moisture but unless you seal the SD card into the socket you'll have a potential for water ingress to the contacts.  I've only dealt with conformal coatings a few times and usually the boards only have pigtails to avoid this sort of issue with connectors.  

That said, I have potted boards with connectors installed for prototype systems and the epoxy never broke the contact. You might be fine installing the final SD cards prior to coating as long as you don't intend to access/remove them.