Yes, the bees don't seem to mind the shape of the hole as long as it has a light blocking back to it. The holes on commercial trays go all the way through and they use a tightly fitted cardboard backing. Some one smarter than me determined that the square holes need more mud to seal and so make the bees work just a little bit harder than those bees using round holes. But yes square holes will work just fine.
RE: I Made This! - Mason Bee Nest