I understand some of what is going on here, but presuming that the issue isn't one of rolling stock being unavailable/crew work requirements, what I don't understand is why the limited services are intentionally timed to be inconvenient. Put another way, if they've got to have the station why not at least try to drag whatever ridership/revenue they can out of the station?
Often these trains are at the bottom of the food chain when it comes to rolling stock and staff. So if there is actually a shortage of staff or of trains, those trains may actually get borrowed for more deserving purposes and the ghost service run some time later as conditions allow. This is probably the better solution that having to cancel some well patronized train at short notice to be able to run a ghost train using the staff and equipment.
If people actually used the trains you would need to apologizse if a train was dirty, or ran late, or was cancelled and this would mean extra costs for the TOC and also suck up management time.