Fluid transport in porous materials is commonly studied in geological samples (soil, sediments etc.) or idealized systems, but the fluid flow through compacted granular materials, consisting of substantially strained granules, remains relatively unexplored. As a step towards filling this gap, we study a model of liquid transport in packings of deformable elastic shells using Finite Element and Lattice-Boltzmann methods. We find that the fluid flow abruptly vanishes as the porosity of the material falls below a critical value, and the flow obstruction exhibits features of a percolation transition. We further show that the fluid flow can be captured by a simplified permeability model in which the complex porous material is replaced by a collection of disordered capillaries, which are distributed and shaped by the percolation transition. To that end, we numerically explore the divergence of hydraulic tortuosity τH and the decrease of a hydraulic radius R h as the percolation threshold is approached. We interpret our results in terms of scaling predictions derived from the percolation theory applied to random packings of spheres.