I vote with onthespot.
If you are worried about reusing cartons, you could easily sterilize the paper ones by putting in the oven for a while. As long as the cartons weren't touching the coils and the temp in the oven is less than 400 degrees, they should be fine. I know you can sterilize potting soil/dirt by baking at 180-200 degrees for 45 minutes. I'd think that would work OK for paper cartons also.
On the other hand, don't try that with stryofoam!
I reuse cartons. I like the paper ones best. People give me cartons all the time once they find out that I've got chickens. And I tell the folks who get my eggs that if they like them they can bring back the carton and the girls will fill it up again. ( I don't sell my eggs, just give them away to friends/family/church/etc). I will throw out any that have any sort of gunk or spillage/water damage though.