Yes, it's just to improve noise immunity. From the datasheet (emphasis mine):
AV CC is connected to the ADC through a passive switch. The internal 2.56V reference is generated from the internal bandgap reference (V BG ) through an internal amplifier. In either case, the external AREF pin is directly connected to the ADC, and the reference voltage can be made more immune to noise by connecting a capacitor between the AREF pin and ground.
So it's just a "nice to have" addition that would have been easy to implement and inexpensive. And for such a small component, I can't see that board space or aesthetics would have been an issue.
As far as software filtering goes, it depends on how much noise is picked up. The battery readings between charged and discharged will only cover a small portion of the total ADC range, so the more accurate the readings are, the better, for determining charge level, time remaining, etc.