Semiconductor-superconductor hybrid systems provide a promising platform for hosting unpaired Majorana fermions towards the realization of fault-tolerant topological quantum computing. In this study we employ the Keldysh nonequilibrium Green s function formalism to model quantum transport in normal-superconductor junctions. We analyze III-V semiconductor nanowire Josephson junctions (InAs/Nb) using a three-dimensional discrete lattice model described by the Bogoliubov-de Gennes Hamiltonian in the tight-binding approximation, and compute the Andreev bound state spectrum and current-phase relations. Recent experiments [Zuo et al., Phys. Rev. Lett. 119, 187704 (2017) and Gharavi et al., arXiv: 1405.7455] reveal critical current oscillations in these devices, and our simulations confirm these to be an interference effect of the transverse subbands in the nanowire. We add disorder to model coherent scattering and study its effect on the critical current oscillations, with an aim to gain a thorough understanding of the experiments. The oscillations in the disordered junction are highly sensitive to the particular realization of the random disorder potential, and to the gate voltage. A macroscopic current measurement thus gives us information about the microscopic profile of the junction. Finally, we study dephasing in the channel by including elastic phase-breaking interactions. The oscillations thus obtained are in good qualitative agreement with the experimental data, and this signifies the essential role of phase-breaking processes in III-V semiconductor nanowire Josephson junctions.