But if you double the length of the sides on the hexagon, then you double the construction cost but quadruple the area. Should we conclude that bees should prefer to make their hives out of a single giant hexagon?
The chamber size is fit to purpose; smaller cells for incubating worker bee larvae, larger cells for drones and queens.
Even for honey and nectar storage, the cells are sized to a single serving (fortunately roughly the same size as a hatchery cell), so the bees can consume what they need while the rest stays safely sealed with wax caps.