I thought they appear for each individual one that you destroy? Some have after I destroyed the turrets, the chest appeared, then I could just climb up and defeat the bokoblins before collecting the treasure chest.
Edit/Update:
So the walkthrough states: Just south of Horseshoe Island there are a pair of platforms. Use your bombs to eliminate the turrets and then climb either of the platforms. Defeat all the enemies and step on the floor switch to cause a treasure chest to appear on the opposite platform. Head on over and defeat the enemies on the other platform and step on another floor switch, causing a treasure chest to appear on the opposite platform. The two treasure chests contain Treasure Chart #43 and a Golden Feather.
I received 20 rupees and a Golden Feather. I did not get a treasure chart. I have not received any charts passed #40 - is there no more than 40 in the GameCube version?