That's exactly why.
The more square/round a box, the less cardboard is used. Less cost.
5 rows x 2 columns would give you 10, but then you have a rectangular box, wasting a lot of cardboard.
3 rows x 3 columns = 9 but it's cheaper to ship more in a single box.
4 rows x 4 columns = 16 could of also worked, but then you probably run into weight issues.
4 rows x 3 columns = 12. The best choice.
Geometry is the same reason why many other things are sold in 6, 12, or 36 packs.
Arithmetic would be a good bit easier in a base 12, or 6 system. Since it divides easily into other numbers.