The pressurisation of the aircraft during takeoff will indeed lead to a (slight) increase in the mass of the air on borard, and therefore the weight of the aircraft.
In cruise, the fact that the aircraft is pressurised means it weighs more than if it was NOT pressurised, but actually less than it did at takeoff, as it has less than sea-level pressure and is thus carrying a smaller mass of air.
I am not aware of this fact being used in any performance calculation, but if it is, it must be incorporated in the charts, as we simply assume the aircrafts weight is it's takeoff weight minus it's fuel burn (or ZFW plus FOB, which is the same thing!)