Zeolites typically contain extra-framework cations to charge-compensate for trivalent Al atom substitutions in the SiO2 framework. These cations, such as Na+, directly interact with quadrupolar guest molecules, such as CO2 and N2, which move through their micropores, causing energetic heterogeneity. To assess the effects of heterogeneity in Na-ZSM-5 on diffusion of CO2 and N2, molecular dynamics (MD) simulations are carried out. In silicalite-1, the pure-silicon form of ZSM-5, the self-diffusivity exhibits a monotonic decrease with molecular loading, while the corrected diffusivity shows a relatively constant value. In contrast, the Na+ cations cause a maximum or a flat profile over molecular loading for the self- and corrected diffusivities of CO2 at T=200 and 300 K, while the cations only have minimal impact on the diffusivity of N2. The MD simulations allow us to identify energy basins or sites at which guest molecules spend a relatively long time, and construct a coarse-grained lattice representation for the pore network. Average residence times at these sites are calculated for both species. The trends observed in the residence times correlate to the trends observed in the diffusivity. The residence times for CO2 at T=200 K are long at low loading, but decrease with loading as additional CO2 molecules compete to stay close to a cation. In contrast, the residence times for N2 are relatively insensitive to the cations, only mildly increasing near a cation. This difference in behavior can be associated to the quadrupole moments of these molecules.