Reliable aerodynamic and aeroelastic design of wind turbines, aircraft wings and turbomachinery blades increasingly relies on the use of high-fidelity Navier-Stokes Computational Fluid Dynamics codes to predict the strongly nonlinear periodic flows associated with structural vibrations and periodically varying farfield boundary conditions. On a single computer core, the harmonic balance solution of the Navier-Stokes equations has been shown to significantly reduce the analysis runtime with respect to the conventional time-domain approach. The problem size of realistic simulations, however, requires high- performance computing. The Computational Fluid Dynamics COSA code features a novel harmonic balance Navier-Stokes solver which has been previously parallelised using both a pure MPI implementation and a hybrid MPI/OpenMP implementation. This paper presents the recently completed optimisation of both parallelisations. The achieved performance improvements of both parallelisations highlight the effectiveness of the adopted parallel optimisation strategies. Moreover, a comparative analysis of the optimal performance of these two architectures in terms of runtime and power consumption using some of the current common HPC architectures highlights the reduction of both aspects achievable by using the hybrid parallelisation with emerging many-core architectures.