This paper studies, from a modelling point of view, the influence of randomly distributed lattice defects (non-patterned areas and variable hole size) on the ferromagnetic resonance behaviour and spin wave mode profiles of 2D magnonic crystals based on Ni80Fe20 antidot arrays with hexagonal lattice. A reference sample is first defined via the comparison of experimental and simulated hysteresis loops and magnetoresistive curves of patterned films, prepared by self-assembly of polystyrene nanospheres. Second, a parametric analysis of the dynamic response is performed, investigating how edge, quasi-uniform and localized modes are affected by alterations of the lattice geometry and bias field amplitude. Finally, some results about the possible use of magnetic antidot arrays in frequency-based sensors for magnetic bead detection are presented, highlighting the need for an accurate control of microstructural features.