In general, I totally agree with you. Unused pads are just a waste of space.
In this case, it's a 10 layer board with blind vias (L1-L5 and L6-L10), where L5 and L6 (in addition to L2 and L9) are plane layers (power and ground). The PCB house complained about missing via pads on L5 and L6. Apparently, they would like pads on start / end layers for the blind vias.