Here are some observations (most might know of these anyways).
In the earlier layouts of the Shrine of the Silver Monkey, you can see the Treasure of Anne Bonny sit on one of the cabinets.
Likewise, the Golden Jaguar of Atahualpa can be seen in the back of the Golden Idols/Treasure Room.
In "The Keys to the Alhambra", when Lisa is in the Tomb of the Ancient Kings, a couple of the golden doors that are usually inaccessible are open and you can see that there is just an empty space behind them.
In "The Golden Earring of Henry Morgan", you can see a piece of construction equipment when Ashley is taken out in the Mine Shaft behind the temple guard door.