We study structural and electronic inhomogeneities in Metal - Organic Molecular monoLayer (OML) - semiconductor interfaces at the sub-nanometer scale by means of in situ Ballistic Electron Emission Microscopy (BEEM). BEEM imaging of Au/1-hexadecanethiols/GaAs(001) heterostructures reveals the evolution of pinholes density as a function of the thickness of the metallic top-contact. Using BEEM in spectroscopic mode in non-short-circuited areas, local electronic fingerprints (barrier height values and corresponding spectral weights) reveal a low-energy tunneling regime through the insulating organic monolayer. At higher energies, BEEM evidences new conduction channels, associated with hot-electron injection in the empty molecular orbitals of the OML. Corresponding band diagrams at buried interfaces can be thus locally described. The energy position of GaAs conduction band minimum in the heterostructure is observed to evolve as a function of the thickness of the deposited metal, and coherently with size-dependent electrostatic effects under the molecular patches. Such BEEM analysis provides a quantitative diagnosis on metallic top-contact formation on organic molecular monolayer and appears as a relevant characterization for its optimization.