As hawkwalk says, there's very little VAT on a package deal through a travel agent anyway but, there would be no refund due anyway since the VAT would be on Thomas Cook's admin fee and that would have been charged at the correct VAT rate at the time. The tax point was the time of the service being provided, not the date you go on holiday.
As for hotel chains refunding VAT on rooms domestically, that will depend on what their deposit policy is. If the deposits are non-refundable then the tax point is the point at which the room was booked and therefore the correct VAT was charged and no refund applies. The hotel would have paid the VAT to the HMRC at 17.5%. If on the other hand deposits are not taken or are refundable then the tax point is the date of supply (when you check in) and, theoretically, VAT would be repayble. We're talking �2.50 in every �117.50 room charge though. In all but the most expensive of hotels it's going to be fairly trivial too. Not worth losing sleep over.