Nanomeshes, often referred to as phononic crystals, have been extensively explored for their unique properties, including phonon coherence and ultralow thermal conductivity (κ). However, experimental demonstrations of phonon coherence are rare and indirect, often relying on comparison with numerical modeling. Notably, a significant aspect of phonon coherence, namely the disorder-induced reduction in κ observed in superlattices, has yet to be experimentally demonstrated. In this study, through atomistic modeling and spectral analysis, we systematically investigate and compare phonon transport behaviors in graphene nanomeshes, characterized by 1D line-like hole boundaries, and silicon nanomeshes, featuring 2D surface-like hole boundaries, while considering various forms of hole boundary roughness. Our findings highlight that to demonstrate a disorder-induced reduction in κ of nanomeshes, optimal conditions include low temperature, smooth and planar hole boundaries, and the utilization of thick films composed of 3D materials.