The concept of a phononic crystal can in principle be realized at the nanoscale whenever the conditions for coherent phonon transport exist. Under such conditions, the dispersion characteristics of both the constitutive material lattice (defined by a primitive cell) and the phononic crystal lattice (defined by a supercell) contribute to the value of the thermal conductivity. It is therefore necessary in this emerging class of phononic materials to treat the lattice dynamics at both periodicity levels. Here we demonstrate the utility of using supercell lattice dynamics to investigate the thermal transport behavior of three-dimensional nanoscale phononic crystals formed from silicon and cubic voids of vacuum. The periodicity of the voids follows a simple cubic arrangement with a lattice constant that is around an order of magnitude larger than that of the bulk crystalline silicon primitive cell. We consider an atomic-scale supercell which incorporates all the details of the silicon atomic locations and the void geometry. For this supercell, we compute the phonon band structure and subsequently predict the thermal conductivity following the Callaway-Holland model. Our findings dictate that for an analysis based on supercell lattice dynamics to be representative of the properties of the underlying lattice model, a minimum supercell size is needed along with a minimum wave vector sampling resolution. Below these minimum values, a thermal conductivity prediction of a bulk material based on a supercell will not adequately recover the value obtained based on a primitive cell. Furthermore, our results show that for the relatively small voids and void spacings we consider (where boundary scattering is dominant), dispersion at the phononic crystal unit cell level plays a noticeable role in determining the thermal conductivity