If you keep firing it on full auto, it'll wear out faster. Moving parts cycling and all that.
I'm not sure it makes too much difference, but also firing full auto when empty means there's no bb in the chamber and less resistance for the piston. It'll thwack the front of the gearbox harder as a result. All gearboxes will crack eventually, so putting undue stress on them will only hasten it's departure!
Just buy a battery dis-charger and save yourself the hassle:
http://www.fire-support.co.uk/product/marui-battery-discharger-new-version