Group III-Nitride-based semiconductor quantum dots (QDs) have attracted much attention in both the fundamental semiconductor physics and in device applications. These semiconductor compounds are formed mostly in the wurtzite structure which introduces a more complex band structure, and strong dependence on strain. Another important characteristic of group III-Nitride compounds is the existence of a large polarization field originating from piezoelectric and pyroelectric polarizations. The charge polarization will create electric fields along the [0001] QD growth axis that will be screened in a complex manner when electrons and holes begin to fill the excited energy levels of the QD during sufficient levels of excitation. In this work, GaN/AlN self-assembled QDs were grown by the Stranski-Krastanov method on a Si(111) substrate. During the growth, a thermal expansion coefficient mismatch between the Si substrate and GaN/AlN film leads to an additional tensile stress which is relaxed by the formation of microcracks. We demonstrate that these microcracks serve as excellent stressors which modify the strain tensor of QDs in their vicinity. The excitonic emission of the QDs with a uniaxial stress perturbation has an in-plane polarization anisotropy. Localized cathodoluminescence (CL) from the QDs exhibits emissions from both the ground and excited states, whose relative contributions depend on the level of excitation. We have studied these emissions using time- and polarization-resolved CL for ensembles of QDs. The effects of screening of the polarization field in the QD, state-filling, changes in the polarization anisotropy and lifetime with excitation are studied both experimentally and theoretically with a 6×6 k·p calculation method. Using the method of ensemble CL, we excite locally groups of QDs subject to a thermal stress perturbation that yields a predictable strain tensor. Varying levels of excitation are employed by adjusting the e-beam current to analyze the effects of carrier filling in the QDs and the resulting emission from excited states. Experimental results indicate that the polarization anisotropy vanishes at high temperatures with an increasing excitation of the QDs, while the anisotropy decreases more slowly with excitation at low temperatures. A theoretical modeling of the effect of carrier filling on the polarization anisotropy and lifetime was also performed, as based on the 3D self-consistent solutions of the Schrödinger and the Poission equations using the 6×6 k·p and effective mass methods for the calculation of the e-h wavefunctions, including the effects of strain perturbation, screening of the QD polarization field, temperature, and occupation of the QD excited sates through changes in the quasi-electron and -hole Fermi levels. These results demonstrate the complex interplay between strain, temperature, and excitation conditions on the polarization dependence of optical emission from an ensemble of wurtzite self-assembled QDs.