How should I treat and store an unused water heater to protect it?
I would be 100% sure that the power is disconnected (or the gas supply and controls are turned off), then drain it completely. Water heaters should be drained annually anyway to purge sediment, so this won't hurt a thing. 

Take precautions to be sure that power won't be reconnected until the heater is completely full of water to avoid damage to heating elements.