Under NEC3-Option-E if the programme is delayed by the Subcontractor and no delay damages have been applied within the contract is there any other way that the Subcontractor can be penalised?
No not really under the contract. You can not impose new sanctions mid contract upon a Subcontractor. The only way to manage Subcontractors in terms of incentivising or penalising to encourage them to meet your contractual requirements for milestones would be through key dates, sectional completion dates, KPI’s and delay damages all of which need to be included within the original tender.
The fact you are option E here you can at least instruct them to do the works in another way with more resources or working double shifts, but you would pay them any cost that they incur and they would get fee on top of that cost. There only risk would be disallowed costs if they spent money that contractually they should not have spent for a reason within 11.2(25).