I have come across a premises that has a W/C and a kitchen which is technically an inner inner room. The MofE is through a store room then a shop. the kitchen is obviously an inner inner room but is there any guidance which allows W/Cs to be located off inner rooms?

No, but an application of common sense and risk assessment is appropriate with rooms/cupboards off an inner room - if a normal habitable room it's a no, but a cupboard or single cubicle toilet could be tolerable as they aren't going to be inhabited for any length of time.