Auto batteries have a couple of ways they may become discharged when stored for a long period of time. If they are in a car, most cars computers and radios will draw a small amount of current to keep the memory active. Normally, this isn't a lot, but can be enough to discharge a battery over a long period of time. Batteries also have a certain amount of self discharge, they will slowly discharge without any load connected.
There is a condition that affects the capacity of the battery called sulfation. It is a layer that is built up on the plates from long periods of discharge caused by a reaction between the lead plates and the sulfuric acid. A quick charge will not remove it, however a long trickle charge can partially restore it. A former auto company engineer gave the example of a battery he had in a seldom used car under this condition, the "green eye" in this car battery would not stay green (indicating a charged battery) even after a quick charge. He put the battery on a trickle charger for a week, and it returned to normal operation. This effect is why it is good to try and determine the date code of any battery you buy in the store, if it has been on the shelf for over a year, it is better to try to find one somewhere else.
Tip: If you are going to have a battery in storage for months at a time in a car, disconnect it from the car, it will reduce the discharge. Or, periodically charge the battery, maybe once every 2 to 4 weeks. If you have it in storage disconnected from the car, a charge every month or two will help keep the self discharge from draining the battery. You may also look for regulated trickle chargers that are designed for this type of application. Thanks to a former auto company engineer for this tip