Optically measuring in the photon counting regime is a recurrent challenge in modern physics and a guarantee to develop weakly invasive probes. Here we investigate this idea on a hybrid nano-optomechanical system composed of a nanowire hybridized to a single Nitrogen-Vacancy (NV) defect. The vibrations of the nanoresonator grant a spatial degree of freedom to the quantum emitter and the photon emission event can now vary in space and time. We investigate how the nanomotion is encoded on the detected photon statistics and explore their spatio-temporal correlation properties. This allows a quantitative measurement of the vibrations of the nanomechanical oscillator at unprecedentedly low light intensities in the photon counting regime when less than one photon is detected per oscillation period, where standard detectors are dark-noise-limited. These results have implications for probing weakly interacting nanoresonators, for low temperature experiments and for investigating single moving markers.