The decarbonisation of short-sea passenger shipping is a central challenge within the broader transition toward intelligent and sustainable transportation systems. This paper presents a model-based design and techno-economic assessment of a Battery Energy Storage System (BESS) retrofitting a hybrid diesel-electric regional ferry operating the Naples-Ischia route (~19 nautical miles). An experimentally validated Equivalent Circuit Model (ECM) of a commercial LiFePO₄ cell, parameterised through Hybrid Pulse Power Characterisation (HPPC) tests at 10 °C, 25 °C, and 40 °C and validated via Extended Kalman Filter State-of-Charge (SOC) estimation, is embedded into a full-vessel dynamic model. This last encompasses propulsion, power generation, electrical distribution and battery subsystems. Two energy management strategies are evaluated against the conventional diesel-electric baseline: Strategy 1 (S1), combining in-port BESS discharge with shore-grid recharging; Strategy 2 (S2), adding controlled in-navigation recharging when SOC falls below 20%. S1 is found to achieve a 17% annual CO₂ reduction, while S2 yields superior 20-year economics, with annual net savings of ~€470,000, a simple payback period of 3.72 years, and ~6 battery replacements versus ~9 under S1. Also, adopting S2 allows maintaining a shallower average Depth of Discharge (DoD), namely ~40% vs. ~70% of S1. A multi-objective optimisation confirms that the proposed BESS layout occupies only 5% of the available garage area and satisfies Load Line Convention constraints without reducing commercial payload capacity. The presented integrated framework provides a replicable, multidisciplinary tool for BESS deployment across the Mediterranean short-sea ferry sector, directly contributing to the advancement of sustainable maritime transportation.