When designing and building Photon Doppler Velocimetry (PDV) systems, single-mode optical fibers (SMF) and components are almost exclusively used due to the additional cost of using polarization maintaining (PM) components and added complexity, as well as the rareness of extremely low amplitude of the beat frequency due to the effect of polarization-dependent loss (PDL). However, the Muller-Stokes method to characterize and measure PDL effects on optical components is a common technique in the telecommunication industry. In this paper, we evaluate the added cost and complexity by developing a 1-channel PDV system with PM components as an example and characterize the effect of PDL using the Muller-Stokes method.