Update: I found an M3x3 screw at a hardware store but it is too wide. I noticed though that the screws used to secure the back case of the Librem 13v2 are the same diameter as the one needed to secure the M.2 card. Do you know what size those screws are? I would guess M2x3?
Update: Confirming that M2x3 wafer head screws indeed fit the M.2 mounting hole. While I couldn’t find any in my local hardware store I was able to order small quantities from http://www.metricscrews.us/.