Vision based control of Unmanned Aerial Vehicles (UAVs) has been adopted by a wide range of applications due to the availability of low-cost on-board sensors and computers. Tuning such systems to work properly requires extensive domain specific experience which limits the growth of emerging applications. Moreover, obtaining performance limits of UAV based visual servoing with the current state-of-the-art is not possible due to the complexity of the models used. In this paper, we present a systematic approach for real-time identification and tuning of visual servoing systems based on a novel robustified version of the recent deep neural networks with the modified relay feedback test (DNN-MRFT) approach. The proposed robust DNN-MRFT algorithm can be used with a multitude of vision sensors and estimation algorithms despite the high levels of sensor's noise. Sensitivity of MRFT to perturbations is investigated and its effect on identification and tuning performance is analyzed. DNN-MRFT was able to detect performance changes due to the use of slower vision sensors, or due to the integration of accelerometer measurements. Experimental identification results were closely matching simulation results, which can be used to explain system behaviour and anticipate the closed loop performance limits given a certain hardware and software setup. Finally, we demonstrate the capability of the DNN-MRFT tuned visual servoing systems to reject external disturbances. Some advantages of the suggested robust identification approach compared to existing visual servoing design approaches are presented.