Carbon nano-onions are a class of nanomaterials that can exhibit long electron spin relaxation times at room temperature and thus hold promise as potential building blocks for spintronics and quantum information processing devices. Despite first being synthesized 30 years ago, there exists a gap in understanding electronic and magnetic properties of these nanostructures. Here we investigate the origin of the metallic-like behavior that has been observed experimentally in disordered nano-onions. Employing a density functional tight-binding approach and starting from ordered multi-shell fullerenes, we develop realistic models of highly disordered nano-onions comprised of nanometer-scale graphitic flakes. We find that multiple parameters such as flake size, edge structure and substituent groups can give rise to in-gap metallic states, effectively closing the HOMO-LUMO gap.