Optical and acoustic resonators utilizing distributed Bragg reflectors (DBRs) are pivotal in advancing technologies ranging from lasers to quantum computing. Under ideal, smooth interface conditions, the efficiency of these resonators, quantified by their quality factor, primarily depends on the number of DBR pairs. However inhomogeneities of the top layer thickness commonly occur, either during growth or fabrication, and is even more severe when a dielectric material is deposited on the top of the samples, for example in responsive resonators. This study analyzes the effects of such inhomogeneities on the resonators' quality factor in the case where the nanometer-scale vertical dimension of the inhomogeneities is significantly shorter than their lateral scale. Employing an analytical approach, we demonstrate that such inhomogeneities can significantly degrade the quality factor, imposing a practical limit to its enhancement irrespective of the DBR pairs added.