Atomically heterogeneous systems, which are created by low energy (0.5 keV) inert gas ion irradiation on metallic surfaces exhibit wetting properties that are characteristically different from those containing physical or patchwise chemical heterogeneities. The wetting properties of such systems are dictated by modification of intermolecular forces by near-surface implanted impurities, leading to a modified effective Hamaker constant. In the present study, special attention is devoted to look at the wetting hysteresis of such systems. It is found that the contact angle is almost a constant in the advancing mode and a finite hysteresis is observed during the receding process, which is believed to arise from liquid retention in the receding mode. We conclude that the nanoscale roughness and the atomic-scale heterogeneities induce negligible pinning and in the receding mode, the solid exhibits a modified effective Hamaker constant which is dependent on the probe liquid. In the advancing mode, however, the effective Hamaker constant is independent of the liquid and depends only on the solid and the embedded ionic species. The evidence of liquid retention has been further validated by a model involving the effective enhancement of surface free energy due to coverage of a thin liquid film.