They should be included, because the price for work done to date includes the costs of these subcontractors – see clauses 11.2(29) and 11.2(23). Of course the answer you come up with for the price adjustment is not added to the price for work done to date, instead it is added to the total of the prices (i.e. the ‘target’) – see clause X1.5.
Option X1 is just a convenient way of calculating an assessment of what the inflation may be, but there are all sorts of ways that the actual inflation can vary from that assessment. However the risks, or rewards, of those variations are shared between the parties through the share mechanism.
In reality, just because there are no inflationary increases within a particular subcontract, it does not mean that the contractor will not be paying for inflation. In that case it could well be (and probably is) the case that there is an allowance for inflation within the subcontractor’s prices.