The WaveTrain device is a wave energy converter concept designed to extend the high performance of buoys that undergo sloped motion into a deep water environment. It achieves this by mechanically interconnecting a series of sloped modules, amongst which restorative forces can be exchanged in order to prevent detrimental pitching motion, whilst sufficiently free motion along the inclined axis is retained. Importantly, this circumvents the requirement of a rigid seabed connection, but introduces a potential vulnerability of operational failure of the rotational joints that link each connecting strut to the adjacent module. In this paper, the impact of considering the fatigue damage accumulating at the joints, in addition to the power extraction, is investigated with regards to the optimal design of the WaveTrain device. A specially-tailored multi-objective genetic algorithm is used to explore the optimal design candidates with two variants of the pair of conflicting objectives (power extraction and fatigue damage). Some key design criteria are then presented, with reference and comparison to the design criteria that are considered optimal when only power extraction is considered.