I think my original post was a bit scatterbrained so let me try to clarify. It takes time to take trains out of service for fumigation purposes, around 5 mins or so for each train (depending on crew size). Assuming you were to end them at Jamaica, it still clogs up service because there are through running trains. Sending the train to LIC/Hunterspoint alleviates that issue because it keeps the train moving. So regardless of if they carry passengers or not, they might as well run them to LIC/Hunterspoint, just so they don't take up valuable time and track space at Jamaica.
With ESA opening up, it's not allowing more flexibility to the railroad in terms of the diesels at all, so the issue becomes where do we send them without affecting service? LIC and Hunterspoint are treated as peak only terminals as it is, there's really no cost to the MTA in just maintaining the service there and the bonus is that we get to store some trains there as well for PM peak. You can't really send them all to Penn either, it's a non-starter because it adds more risk to one of the diesels breaking down in there and the fact that the Dual-Electric locos can't go there.