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The effects of cobalt incorporation in spherical heterostructured iron oxide nanocrystals (NCs) of sub-critical size have been explored by colloidal chemistry methods. Synchrotron X-ray total scattering methods suggest that cobalt (Co) substitution in rock salt iron oxide NCs tends to remedy its vacant iron sites, offering a higher degree of resistance to oxidative conversion. Self-passivation still creates a spinel-like shell, but with higher volume fraction of the rock salt Co-containing phase in the core. The higher divalent metal stoichiometry in the rock salt phase, with increasing Co content, results in a population of unoccupied tetrahedral metal sites in the spinel part, likely through oxidative shell creation, involving an ordered defect-clustering mechanism, directly correlated to the core stabilization. To shed light on the effects of Co-substitution and atomic-scale defects (vacant sites), Monte Carlo simulations suggest that designed NCs, with desirable, enhanced magnetic properties (cf. exchange bias and coercivity), are developed with magnetocrystalline anisotropy raised at relatively low content of Co ions in the lattice. Growth of optimally performing candidates combines also a strongly exchange-coupled system, secured through a high volumetric ratio rock salt phase, interfaced by a not so defective spinel shell. In view of these requirements, Specific Absorption Rate (SAR) calculations demonstrate that the sufficiently protected from oxidation rock salt core and preserved over time heterostructure, play a key role in magnetically-mediated heating efficacies, for potential use of such NCs in magnetic hyperthermia applications., Main text of 23 pages, 12 Figures. Supplementary Information of 17 pages, 9 Figures, 4 Tables