The mod only does anything at the moment the resource runs out. It could leave behind the chest forever if it is not empty, but it wouldn't be empty because the last ore was just put into it. It would take a lot more logic to remember which chests should be removed and check if they are empty yet.
This feature is in place in 0.4.0! It will wait up to 30 seconds for the chest to empty before decontruction, or for pending logistic pickups to complete.
