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Isotopologue line intensity ratios of circumstellar molecules have been widely used to trace the photospheric elemental isotopic ratios of evolved stars. However, depending on the molecular species and the physical conditions of the environment, the circumstellar isotopologue ratio may deviate considerably from the stellar atmospheric value. In this paper, we aim to examine how the CO and HCN abundance ratios vary radially due to chemical reactions in the outflows of AGB stars and the effect of excitation and optical depth on the resulting line intensity ratios. We find that the circumstellar 12CO/13CO can deviate from its atmospheric value by up to 25-94% and 6-60% for C- and O-type CSEs, respectively. We show that variations of the intensity of the ISRF and the gas kinetic temperature can significantly influence the CO isotopologue ratio in the outer CSEs. On the contrary, the H12CN/H13CN ratio is stable for all tested mass-loss rates. The RT modeling shows that the integrated line intensity ratio of CO of different rotational transitions varies significantly for stars with intermediate mass-loss rates due to combined chemical and excitation effects. In contrast, the excitation conditions for the both HCN isotopologues are the same. We demonstrate the importance of using the isotopologue abundance profiles from chemical models as inputs to RT models in the interpretation of isotopologue observations. Previous studies of CO isotopologue ratios are based on multi-transition data for individual sources and it is difficult to estimate the errors in the reported values due to assumptions that are not entirely correct according to this study. If anything, previous studies may have overestimated the circumstellar 12CO/13CO abundance ratio. The use of the HCN as a tracer of C isotope ratios is affected by fewer complicating problems, provided one accounts corrections for high optical depths.