Nanoscale inhomogeneities and impurity clustering are often found to drastically affect the magnetic and transport properties in disordered/diluted systems, giving rise to rich and complex phenomena. However, the physics of these systems still remains to be explored in more detail as can be seen from the scarce literature available. We present a detailed theoretical analysis of the effects of nanoscale inhomogeneities on the spin excitation spectrum in diluted magnetic systems. The calculations are performed on relatively large systems (up to N = 66(3)). It is found that even low concentrations of inhomogeneities have drastic effects on both the magnon density of states and magnon excitations. These effects become even more pronounced in the case of short-ranged magnetic interactions between the impurities. In contrast to the increase of critical temperatures T-C, reported in previous studies, the spin-stiffness D is systematically suppressed in the presence of nanoscale inhomogeneities. Moreover D is found to strongly depend on the inhomogeneities' concentration, the cluster size, as well as the range of the magnetic interactions. The findings are discussed in the prospect of potential spintronics applications. We believe that this detailed numerical work could initiate future experimental studies to probe this rich physics with the most appropriate tool, inelastic neutron scattering.