I had a cart disappear once, it might have been back around the time of the 5.2.1 update but I think that that would have occurred to me if it had happened at exactly that time. Or maybe I just didn't notice that it was missing for a while afterwards. It was on the surface so lightning is also a possibility, but the number of people saying that underground carts also disappear, and it happening regularly so it can't be a pack update, leads me to conclude that it's just falling through the world like golems sometimes do. Back in vanilla when the only automation I had was a pack of attack dogs, I would sometimes be running back to my base when suddenly a dozen wet dogs all appear next to me. I can only conclude that they were falling through the world as a chunk started to load and ended up landing in an underground lake and then teleporting to me. Also, occasionally a whole load of my dogs would vanish for no good reason. Falling through the world, must be.