Another cause of soft-shelled eggs can be physical stress to the point that the eggs move through too quickly. I had a hen start laying soft shells even though she was eating layer feed and had calcium available free-choice. It obviously wasn't a calcium deficit. She laid three soft-shelled eggs and then stopped laying and acted withdrawn and puffy so I did some sleuthing. It turned out she had worms and just needed a few days of treatment to get back to herself. So, I vote to keep a close watch because they can decline rapidly.
ETA: Forgot to mention that missing eggs can be a sign of predators stealing from your nests. Snakes, in particular, can steal eggs without leaving a trace that they've visited. A thieving human can empty all of the nests quite efficiently...