The dimer Mott insulator \(\kappa\)-(BEDT-TTF)\(_2\)Cu\(_2\)(CN)\(_3\) exhibits unusual electrodynamic properties. Numerical investigations of the electronic ground state and the molecular and lattice vibrations reveal the importance of the Cu\(_2\)(CN)\(_3^-\) anion network coupled to the BEDT-TTF molecules: The threefold cyanide coordination of copper and linkage isomerism in the anion structure cause a loss of symmetry, frustration, disorder, and domain formation. Our findings consistently explain the temperature and polarization-dependent THz and infrared measurements, reinforce the understanding of dielectric properties and have important implications for the quantum spin-liquid state, which should be treated beyond two-dimensional, purely electronic models.