Long trains are less reliable - more cars and more intense dynamic forces in the train to cause equipment problems. And long trains are a lot slower to handle in yards without large investments in long arrival/departure tracks. With loosely scheduled freight trains, 2 short trains/day produce much more predictable origin-to-destination trip times for freight shipments than 1 long, which is what customers care about.
Hunter's innovation was to finally get RR operating departments to run freight to schedule. If freights are on time, meets can be planned for a few double-track segments or lengthened sidings, and time/space to double or triple a train out of the yard that can't be enlarged can be allowed for. Cars will tend to sit longer in yards waiting for infrequent trains, but longer trips times are less important than predictability to customers the RRs have kept through the 1970s, 80s and 90s. And RRs have had crew costs first on the list of places to cut since long before I was born.