The boxes are delivered to the shop as a pre-cut sheet of cardboard which is then folded into shape. If you can design a circular box which can be stored flat, ready for subsequent folding, you'll have developed a whole new branch of mathematics!
Our pizza comes in an octagonal box and clearly slides round less than the normal square boxes, as most of the topping is still somewhere near the pizza
Also, traditionally, pizzas were spun to get them the right shape. Hence, round pizzas are the easiest to make and so are square boxes. Still, it'd be better if the pizza actually fit in the box properly.
I cant remeber which chain I got it from but I remeber opening my pizza box once to find that my pizza had been 'stapled' to the base of the box with some kind of plastic pin. Ingenius, although slighty unappetising.