The work considers the effect of extraordinary optical transmission (EOT) in polycrystalline arrays of nanopores fabricated via nanosphere photolithography (NPL). The use of samples with different qualities of polycrystalline structure allows us to reveal the role of disorder for EOT. We propose a phenomenological model which takes the disorder into account in numerical simulations and validate it using experimental data. Due to the NPL flexibility for the structure geometry control, we demonstrate the possiblity to partially compensate the disorder influence on EOT by the nanopore depth adjustments. The proposed experimental and theoretical results are promising to reveal the NPL limits for EOT-based devices and stimulate systematic studies of disorder compensation designs.