Very interesting theories here!
For the OP, I don't like the idea of food spoilage, because it'd then likely be a tedious mini game. Lost some food to the spoilage - forced to partial rest - need to find/buy some food -. need to rest again to recover spells etc.
I like JandK's exhaustion suggestion. Lets say you get some minor penalty after short resting. Short rest is a desired thing to use frequently because it recharges a lot of actions and some spells + convenient healing. So you won't be able to just ignore short rests completely.
