Hexagons are what you get when you squish a lot of semi-rigid round things together. It's not like the bees are designing hexagons - look at the cells on the free edges of a comb and you'll see little in the way of sharp hex-ey corners
it's hard to say what "designing" means - is a box-packing algorithm "designing" the packing pattern when it runs? Or is it just following a series of algorithmic steps "blindly" and yet, being able to reach an outcome that has certain properties (like being very densely packed)?