We have two male hamsters in separate cages and we let them run (separately) in a blanket chest that has sand and toys in it. When they get in, they sniff around and then seem to scent-mark everywhere by rubbing their bodies on things. They seem active and interested and not stressed by the smell of the other. They run around the house in separate balls and take no notice of each other. So, my question is… is the use of the same blanket chest for two different hamsters causing them stress that I can't see and is it cruel?

no i don't think it's cruel- they might like smelling these other smells of a hamster :] it might make their play time a bit more interesting by following a scent, i think it's really nice how concerned you are about your hamsters though xD <3