Hydrogen fueled Polymer Electrolyte Membrane Fuel Cells/Lithium-Ion Battery powertrains could be a promising solution for zero-local-emission shipping. The power allocation between PEMFC and LIB and their respective performance degradation play a crucial role in reducing the powertrain operating and maintenance costs. While several research works proposed energy management strategies to face these issues, a long-term operation optimization including the uncertainty in the input parameters of the model has not been extensively addressed. To this purpose, this study couples an operation optimization model of a PEMFC/LIB ferry propulsion system with a Monte-Carlo analysis to investigate the influence of PEMFC, LIB and hydrogen costs on the optimal operation of a hydrogen-powered ferry in the long-term. Hydrogen cost results to be the most influent parameter, in particular toward the end of the plant lifetime, when hydrogen consumption increases by up to 30%. Nevertheless, the variability of optimal ferry operation gradually decreases with the progressive PEMFC/LIB degradation.