I expect that the reason is that the gift shop, being attended, offers better security. However, security might not be an issue, since no one in their right mind would donate to the museum by leaving anything valuable in the recycle container. For example, a Nikon D90 digital camera is an item on the recycle list for which they offer $10. These cameras have sold on eBay for $1,000, so recycling a valuable item makes no sense.
-John