In this work, we focus on the early design phase of cruise ship hulls, where the designers are tasked with ensuring the structural resilience of the ship against extreme waves while reducing steel usage and respecting safety and manufacturing constraints. At this stage the geometry of the ship is already finalized and the designer choose the thickness of the primary structural elements, such as decks, bulkheads, and the shell. Reduced order modeling and black-box optimization techniques reduce the use of expensive finite element analysis to only validate the most promising configurations, thanks to the efficient exploration of the domain of decision variables. However, the quality of the final results heavily relies on the problem formulation, and on how the structural elements are assigned to the decision variables. With the increased request for alternative fuels and engine technologies, the designers are often faced with novel configurations and risk producing ill-suited parameterizations. To address this issue, we enhanced a structural optimization pipeline for cruise ships developed in collaboration with Fincantieri S.p.A. with a novel data-driven hierarchical reparameterization procedure, based on the optimization of a series of sub-problems. Moreover, we implemented a multi-objective optimization module to provide the designers with insights into the efficient trade-offs between competing quantities of interest and enhanced the single-objective Bayesian optimization module. The new pipeline is tested on a simplified midship section and a full ship hull, comparing the automated reparameterization to a baseline model provided by the designers. The tests show that the iterative refinement outperforms the baseline, thus streamlining the initial design phase and helping tackle more innovative projects.