Asus conducted a series of internal tests and confirmed that overheating of the ROG Ally can indeed lead to problems with the MicroSD card reader. The company assured that the hardware issue is solvable with a software update that will calibrate the system fan rotation speeds.
It is worth noting that the memory card reader on Asus’s handheld gaming device is located next to the heat exhaust vent, so it is unlikely that the hardware problem can be solved by a system update.