A coupled numerical scheme, based on modal expansions and boundary integral representations , is developed for treating propagation and scattering by dense arrays of impenetrable cylinders inside a waveguide. Numerical results are presented and discussed concerning reflection and transmission, as well as the wave details both inside and outside the array. The method is applied to water waves propagating over an array of vertical cylinders in constant depth extended all over the water column, operating as a porous breakwater unit in a periodic arrangement (segmented breakwater). Focusing on the reflection and transmission properties, a simplified model is also derived, based on Foldy-Lax theory. The latter provides an equivalent index of refraction of the medium representing the porous structure, modeled as an inclusion in the waveguide. Results obtained by the present fully coupled and approximate models are compared against experimental measurements, collected in wave tank, showing good agreement. The present analysis permits an efficient calculation of the properties of the examined structure, reducing the computational cost and supporting design and optimization studies.