If memory serves me correctly, the M12 series also uses two fans 120mm and 60mm. The S12 only uses one fan.
Therefore, the M12 in general is a little louder than the S12 series. I'm a stickler for noise so I'd rather buy the S12 series than the M12 series. In fact, I bought two S12 PSUs in the past 5 years.
It boils down to if you want a modular PSU to detach cables you don't need for better cable management, or a quieter PSU with no detachable cables.