If a business pays compensation for poor service, that is a cost to the business which can readily be measured. If a customer stops purchasing from that business, or is deterred from buying in the first place, that is also a cost, but one that is much harder to measure.
You appear to be assuming that the only impact of Delay Repay is in the cost of what train operators pay. You therefore ignore the other side of the ledger, and the gains that companies make from retaining customers who’d otherwise leave, or not even travel.
I always claim Delay Repay if eligible, because it is my entitlement under the contract I’ve entered into. There’s no question of fault, and I don’t care as a customer whether it is due to the operator, another operator, Network Rail, or a rogue pheasant. But it does make me more likely to make discretionary journeys, and does give irregular travellers greater confidence that they will be treated fairly.
So I’d ask a different question - what would it cost the railway in lost revenue not to pay Delay Repay?