This paper presents a nonlinear frequency domain model and uses this to assess the performance of a wave energy converter (WEC) array with a nonlinear power take-off (PTO). In this model, the nonlinear PTO forces are approximated by a truncated Fourier series, while the dynamics of the WEC array are described by a set of linear motion equations in the frequency domain, and the hydrodynamic coefficients are obtained with the boundary element method. A single heave absorber is firstly investigated to establish the accuracy of the new model in capturing the nonlinear behaviour of the pumping system. Subsequently, simulations of a 2D array with 18 WECs and a pillar in the centre (representing the tower of a wind turbine) are carried out to understand wave interference effects. Several optimisation strategies are proposed to improve the overall performance of the WEC array. These results demonstrate a computationally effective method for accounting for nonlinear effects in large WEC arrays. The proposed approach may potentially be applied for developing control algorithms for the adaptability of a 2D array to incoming wave excitation.