This work focuses on the emission processes of metal-organic clusters MmMen, (M is the organic molecule and Me the metal atom) ejected from self assembled monolayers (SAMs) of alkanethiols on gold after keV ion bombardment. These aggregates are often observed upon energetic ion bombardment of strongly bound molecules like SAMs. The explanation of this effect remains elusive, especially for large clusters as those observed in our study. The emission of these clusters is investigated using ToF-SIMS under 15 keV Ga+ bombardment. In particular, we have measured the energy distributions (KEDs), which are informative of the physical processes of sputtering. We have probed both the influence of the intermolecular forces and the adsorbate-metal bonding on the cluster ion emission. Importantly, our KEDs revealed that a significant fraction of MmMen clusters is formed via the metastable decay of larger aggregates in the acceleration section of the spectrometer. This is the experimental evidence that another cluster formation channel has to be considered in addition to the recombination mechanisms proposed by other groups. In parallel to these experiments, we have used classical molecular dynamics (MD) simulations to model an overlayer of octanethiols on gold. A realistic potential has been used including long-range forces between the hydrocarbon chains of the alkanethiols. Our key finding concerns the emission of large clusters which were not observed under sub-keV projectile impact. Statistically, they are predominantly formed in high yield events, where many fragments and (supra)molecular species are ejected. From the microscopic viewpoint, these events mostly stem from the confinement of the projectile and recoil atom energies in a finite nanovolume of the surface. As a result of the high local energy density, molecular aggregates desorb from an overheated liquid-like region surrounding the impact point. In summary, from a combined experimental and computational study we have shown that analytical models involving linear collision cascades and recombination processes are insufficient to describe metal-thiolate cluster emission from SAMs under keV ion bombardment. The detailed MD investigation have allowed us to obtain a general picture of the emission of these aggregates in which the mechanisms at play are reminiscent of those high yields events (megaevents) with non linear effects used usually to account for large (bio)molecule desorption.