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Recent experiments with strong THz fields in both conventional and unconventional superconductors have clearly evidenced a marked third-harmonic generation below the superconducting temperature $T_c$. Its interpretation challenged substantial theoretical work aimed at establishing the relative efficiency of quasiparticle excitations and collective modes in triggering such a resonant response. Here we compute the non-linear current by implementing a time-dependent Bogoljubov de-Gennes approach, with the twofold aim to account non-perturbatively for the effect of local disorder, and to include the contribution of all collective modes, i.e. superconducting amplitude (Higgs) and phase fluctuations, and charge fluctuations. We show that, in agreement with previous work, already at small disorder the quasiparticle response is dominated by paramagnetic effects. We further demonstrate that paramagnetic processes mediate also the response of all collective modes, with a substantial contribution of charge/phase fluctuations. These processes, which have been overlooked so far, turn out to dominate the third-order current at strong disorder. In addition, we show that disorder strongly influences the polarization dependence of the non-linear response, with a marked difference between the clean and the disordered case. Our results are particularly relevant for recent experiments in cuprates, whose band structure is in a first approximation reproduced by our lattice model.