On a 1999 Silverado Pickup there are two holes on both front corners of the cargo box between the bed and the cab. I don't mean the stake pockets. If you run your fingers along the forward top edge you can locate them. When you put on a lid or a cap it will not be water tight. Is Chevrolet going to correct this?
I wouldn't expect a recall anytime soon. Go take a closer look at the cargo box on your Silverado. The holes that you're describing do not go through to the interior of the box at all. They are open to the area between the exterior body panel and the side cargo box wall. This area is wide open at the bottom, and we're fairly confident that the holes were either a part of the manufacturing process and/or were used for ventilation purposes.
Let's remember that pickup trucks were not designed to float. You may notice it also has drain holes in the corners. Installing a cap will keep the bed interior dry unless the water level reaches the door handles.