We discuss in two companion papers how Fourier-space measurements may be coupled to rheological tests in order to elucidate the relationship between mechanical properties and microscopic dynamics in soft matter. In this second companion paper, we focus on Differential Dynamic Microscopy (DDM) under shear. We highlight the analogies and the differences with dynamic light scattering coupled to rheology, providing a theoretical approach and practical guidelines to separate the contributions to DDM arising from the affine and the non-affine part of the microscopic displacement field. We show that in DDM under shear the coherence of the illuminating source plays a key role, determining the effective sample thickness that is probed. Our theoretical analysis is validated by experiments on 2D samples and 3D gels.