The only "problem" with stacking the cages is that you'd need to cut out the sides of the bottom one. In a single story cage, people do it, but it's really not necessary. Leaving the side cut-outs out of the design keeps the cage a lot more chew-proof (and cheaper and easier to make, because the bins are usually a thicker plastic than the lids). The ventilation holes and the top cut-outs are really all you need normally, so if you wanted to have less work, I'd just cut out the walls on the bottom one and leave the top one's side's alone (except for the holes).
