Visible crew/equipment: On Skull Island, when Carl says, "No one has lived here for hundreds of years," the distinctive reflection of the scrim/reflector screen is visible in the lens of Preston's glasses, as he looks down; there are other moments in the film where this happens with characters' eyeglasses.
Visible crew/equipment: As one of the Venture crew members picks up a chloroform bottle from a case, you can see a bright studio spotlight reflected in the bottle.
Answer: They scared them off with their guns. In the scene where they capture Ann to sacrifice her to Kong, Denham and his men come to rescue her and when they start shooting the natives hide. It's never fully explained but the most likely answer is that they are too scared and have even moved villages or are just hiding really well.