Space based quantum technologies are essential building blocks for global quantum networks. However, the optoelectronic components and devices used are susceptible to radiation damage. The SpooQy-1 CubeSat mission demonstrated polarization-based quantum entanglement correlations using avalanche photodiodes for single-photon detection. While predicting instrument performance remains a challenging part of space missions, here, we report on how in-situ dark count rate trends of two silicon Geiger-mode avalanche photodiodes (GM-APD) may be predicted using high-fidelity radiation modelling techniques. This aids the diagnosis of unexpected trends in instrument performance as we were able to support the claim that differences in radiation shielding was a major contributor to the observed in-orbit data. While low-fidelity modelling is limited to lifetime predictions, implementing high-fidelity radiation modelling can have applications beyond this for low-earth orbit CubeSats.