Batteries use mAh because it is a unit of electric charge. Amps and hours are more easily understood than joules. Joule is a unit of energy where energy = voltage * charge, and voltage is something you can alter with transformers, power regulators, placing batteries in series etc. It is also (supposed to be) constant for batteries of the same type, and those things makes the voltage factor redundant for comparing battery capacity.
BTW, to convert between V*mA*h and Joule you would also have to multiply with a constant with several decimal places.
