The answer is that they can work, at least sometimes, and to some extent. Consider, for instance, rigid molecules with no rotatable bonds and only one conformation. In such cases, conformational strain energy plays no role; it isn't even defined with only one conformation. If the protein-ligand binding free energy is reasonably estimated as the sum of the intermolecular interactions and desolvation energies in the scoring function, the docking program can identify important drugs correctly or at least quasi-correctly. The geometry of these important drugs may have high strain, but using the true realistic geometry, the interaction between the protein and ligand, as well as the desolvation energies, would be about the same. In other words, the protein-ligand binding free energy for the non-physical, highly strained geometry and the realistic geometry of the given molecule is roughly the same, making the choice of geometry less critical.