In this study, we investigate structural disorder and its implications in metal cluster (MC)-based compounds, specifically focusing on Cs2[{Mo6Xi8}Xa6] (X = Cl and Br). Utilizing synchrotron radiation X-ray diffraction, Fourier transform infrared spectroscopy, and luminescence measurements, we examined the incorporation of water molecules into these compounds and their effects on the crystal structure and optical properties. Our findings reveal that the presence of water molecules induces the lattice disorder, particularly the displacement of Cs atoms. Density functional theory calculations, including dispersion corrections (DFT-D), were employed to model superlattices incorporating varying positions and amounts of water molecules. The DFT-D results corroborated experimental data, indicating that water molecules notably impact the lattice structure by causing the Cs disorder without altering the fundamental trigonal arrangement of MC units. Our results reveal that the composition of the compounds, specifically the Cs/[{Mo6Xi8}Xa6] ratio, remains stoichiometric, regardless of the amount of water in their lattice. Luminescence spectroscopies confirmed that the water incorporation and the lattice disorder had little effect on the luminescence wavelength, but purification enhanced the luminescence efficiency. This study highlights the importance of understanding structural disorders in MC-based compounds for optoelectronic applications and demonstrates the utility of DFT calculations in exploring complex crystallographic phenomena.