Zinc oxide (ZnO) nanostructures were synthesized in the form of nanoparticles, nanoflowers and nanourchins. Structural, electronic and optical characterization of the samples was performed via standard techniques such as X-ray diffraction (XRD), scanning electron microscopy (SEM), photoluminescence, Raman and ultraviolet-visible (UV-Vis) spectroscopy. Point defect structures which are specific to each morphology have been investigated in terms of their concentration and location via state-of-the-art electron paramagnetic resonance (EPR) spectroscopy. According to the core-shell model, all the samples revealed core defects; however, the defects on the surface are smeared out. Finally, all three morphologies have been tested as electrode materials in a real supercapacitor device and the performance of the device, in particular, the specific capacitance and the storage mechanism, has been mediated by the point defects. Morphology-dependent defective ZnO electrodes enable the monitoring of the working principle of the supercapacitor device ranging from electric double-layer capacitors (EDLC) to pseudo-supercapacitors.