c-Si/a-Si:H-based solar cells are characterized by impressive efficiencies for silicon based devices. In this paper, we present a comprehensive atomistic simulation study of the structural and transport properties of crystalline silicon and hydrogenated amorphous silicon heterostructures for photovoltaic applications. By leveraging state-of-the-art molecular dynamics simulations with a machine-learned force field, we explore the effects of thermal boundary resistance as well as hydrogen diffusion on device performance. The simulations reveal the dependence of thermal properties on crystalline orientations, cooling rates of the amorphous layer, and interface morphology. A systematic investigation of hydrogen diffusion demonstrates its impact on heat transport and structural stability, highlighting the role of moderate hydrogenation (≤ 10%) and specific orientations in enhancing thermal dissipation and reducing degradation. These findings provide atomistic insights into optimizing c-Si/a-Si:H interfaces, enabling improved thermal management and long-term stability for high-performance solar cells.