I agree, unless you keep it entirely dry and free of plants or anything else, the wood chips will not be sterile for very long. If you've had that atrium for 18 years and never seen a bug or a fungus, something's being done to prevent them.
Does somebody take care of the atrium for you? Maybe they spray the wood chips with fungicide and insecticide regularly? If so, then you can just go ahead and get some new bagged wood chip mulch and put it down, then let your maintenance crew know to spray the next time they come. Rubber chip mulch smells rubbery for months and months after you lay it down. You don't want that in your house. Stones would be the cleanest mulch you could put down, but they're heavy, expensive and if you have plants planted in the soil in there, the stones are not a good mulch for plants. They tend to heat up the soil instead of cooling it down, and don't insulate well or retain moisture either.
