In this paper, we investigate the disruptive effects of solar scintillation in Deep Space Networks (DSNs) and we apply Network Coded Cooperation (NCC) in DSNs to improve the throughput, the robustness and the security of the communication systems. Simulations illustrate the comparisons between direct links and NCC links for both Rayleigh and Rician fading channel models. The effects of solar scintillation are modelled based on previous studies and the outage probabilities of these links are given. In addition to the computer simulations, the proposed system model is implemented with Software Defined Radio (SDR) nodes and the error performances are illustrated with Bit Error Rates (BER) and Signal-to-Noise Ratios (SNR) metrics. Based on simulation and test results, it can be seen that NCC systems can decrease the outage probability, improve the error performance, and also decrease the transmission time between transmitters and receivers.