They could have put 1 & 2 on the side of the first and second seasons, and three on this one. BEsides if it was in volumes, it would say Scooby Doo, Where Are You Volume 2.
Agree that it's a bit awkward, in that the spine number refers to the DVD set number, rather than the Season. Which is why the first set was only labelled "1" even though it contained Season 1 *and* 2.