Yes for cooling reasons on most amps, but that is if you play them for hrs and hrs on end.
The grommets or rubber pads between the box and sub help to dampen unwanted vibration transfering to the amps internals, lessing the life of the amp.
As another mentioned. It is easier to still if this is done, but makes it easier to install in most cases, and also frees up room for those cars that have little room.