Considerations to decarbonize maritime shipping by implementing the Emissions Trading System (ETS) are underway at the International Maritime Organization (IMO). This study seeks to investigate the impact of ETS on short-term fleet deployment decisions of liner shipping companies. Considering pragmatic scenarios of demand uncertainty and transshipment, we extend state-of-the-art maritime operational planning under climate policies and propose a fleet planning model accounting for carbon emissions to evaluate the decision-making nuances of a liner company. Numerical experiments are conducted to analyze ETS implementations with varying policy design parameters for their efficacy in mitigating emissions and potential impact on stakeholders. The findings indicate that, for liner shipping which is cross-regional by nature, regional ETS implementations are inadequate due to carbon leakage; the efficacy of open ETS policies is limited, particularly when carbon prices are low; strict carbon purchase caps integrated with robust carbon price-setting mechanisms are critical to designing an effective ETS.