The lighter seems to have been empty - the war diary seems to confirm it. If it was loaded, it would sit lower in the water. Empty it is easier to move it or for it to drift. Sailors could have pulled it into a new position. We used to do the same when using barges to paint the side of CVN-65. If it was loaded, a tug would have been needed to move it. If it was empty, it would have made sense to try to use it to protect the sides.

The lighter cover appears to be canvas. It could be sheet metal, but my bet is canvas. The topside view shows crossmembers to support the canvas. If it was canvas - and the point of the cover was to keep the ammo cooler in the tropical sun - then it would not take much to damage it. Perhaps debris or shockwaves.