Part of it is due to the safety features implemented in Lithium-ion batteries. There is actually a circuit board within the battery so if the battery cells become completely depleted it may prevent the battery from charging. I'm not entirely sure of the specific details of why it fails to charge. This can happen with any Lithium-ion battery and is not an Apple specific issue.
Then there is the Apple specific issue with the Logic Board where if there is a battery problem it can prevent the laptop from powering on. Apple laptops pull power from the battery even when the charger is being used which helps to filter a bad electricity source so it is less likely to damage the Logic Board. So if there is an issue with the battery it creates a power issue with the whole system which means the Logic Board won't have the necessary power to turn on even when using the charger.
While you should generally be Ok if the battery drains to 0% for a short time, however, extended periods can cause damage to the battery in addition to the other issues mentioned. I personally would try not to leave the battery at 0% overnight.