We investigate native defects and their impact on the electronic structure of Td-MoTe2 and graphene/Td-MoTe2 van der Waals heterostructures using scanning tunnelling microscopy and spectroscopy. STM reveals a high density of circular, hollow surface defects that we attribute to Te vacancies. STS on pristine MoTe2 shows semimetallic, V-shaped dI/dV spectra with subtle low-energy states. The vacancies suppress the tunnelling conductance below the Fermi level without introducing new sharp defect-related resonances, consistent with a vacancy-induced redistribution of Mo-Te spectral weight rather than the appearance of new electronic states. In the heterostructure, graphene preserves these MoTe2 fingerprints with no noticeable graphene doping or charge transfer. Our results demonstrate that isolated native Te vacancies act as spectroscopically weak perturbations to the low-energy electronic structure of graphene. The graphene overlayer further screens their impact on the electronic structure, making graphene/Td-MoTe2 heterostructures intrinsically tolerant to such interface defects.