Naval ship design must balance multiple conflicting requirements, including the need for fast response times and high speeds, often leading to large and complex hybrid propulsion systems. At the same time, the decarbonisation of ship operations and the shipping industry has become one of the most concerning topics for the maritime community. Even if the military sector has not been driven yet by this regulatory framework, decarbonisation is also becoming a hot topic for the navies. Additionally, short-term power loads encompass numerous demanding applications. The impact of this type of load on the performance of the shipboard power system influences power quality, and load levelling has been proven to be one of the critical power management strategies for new naval shipboard electric plants. Furthermore, decarbonisation and electric pulse management require pervasive automation systems to balance reduced crew sizes effectively. In recent years, Battery Energy Storage Systems (BESS) have emerged as effective tools for reducing greenhouse gas emissions, as well as for load levelling and peak shaving. These systems support power management strategies, addressing conflicting naval ship design requirements and optimising these critical concerns. BESS-based hybrid propulsion is a promising solution for enhancing the energy efficiency of naval ships. It has been proven to be a reliable and flexible design option for improving the power quality of the electric grid. However, BESS requires space, weight tolerance, and cost expenditures to match all other military operational requirements in one convenient, optimal shipboard power plant. The paper outlines an optimisation-based approach to size a BESS-based hybrid propulsion architecture for naval ships, primarily focusing on reducing environmental footprint, increasing efficiency, and improving power grid reliability. The optimisation aims to minimise the ship exhaust emissions in terms of equivalent CO2. The frontline ship type case study has been analysed while manoeuvring in restricted waters and deep seas in a given pseudo-random operating condition extracted from actual data, showing potential interest in a new, energy-efficient, and resilient solution. For comprehensive benchmarking, the case study has been further examined and discussed with different sizing configurations, and each case study has been ranked with a set of Key Performance Indicators (KPIs). The study shows that, despite the increasing size and weight of the BESS to reduce fuel consumption, analysing different solutions with a model-based strategy for the hybrid plant gives interesting trade-offs during the design phase while leaving space for new research directions.