A quantum-classical protocol that incorporates Jahn-Teller vibronic coupling effects and cluster analysis of molecular dynamics simulations is reported, providing a tool for simulations of absorption spectra and ultrafast nonadiabatic dynamics in large molecular photosystems undergoing aggregation in solution. Employing zinc phthalocyanine dyes as target systems, we demonstrated that the proposed protocol provided fundamental information on vibronic, electronic couplings and thermal dynamical effects that mostly contribute to the absorption spectra lineshape and the fluorescence quenching processes upon dye aggregation. Decomposing the various effects arising upon dimer formation, the structure-property relations associated with their optical responses have been deciphered at atomistic resolution.