Why do cones pit in hub bearings?
According to my research, which consists of a couple of web searches and looking at a few photos, the failure mechanism that causes pits in bearing cones is spalling. It is the result of metal fatigue from balls repeatedly rolling over the same part of the cone, and it can be recognized by the irregular shape of the pits. This is different from mechanical wear, which produces a smooth groove and brinelling, which produces smooth indentations at even intervals.
The reason why cone is affected first is that the load is concentrated on smaller surface. The inner diameter of the bearing is smaller than the outer bearing, so the surface is smaller to begin with, and in bicycle wheels the cone does not rotate so the load is concentrated on a small part at the lower side of the cone. Because the outer race rotates, the load is spread to the entire bearing track. The quality of materials has also some effect here: I have seen this damage only on two Alivio hubs. The cheap no-brand cup and cone hubs that I have seen had a worn groove at the bottom side of the cone, and I have not had cone failures in higher tier hubs.