Bayesian Networks (BN) are probabilistic models that are commonly used for the diagnosis in numerous domains (medicine, finance, transport, robotics, …). In the case of autonomous vehicles, they can contribute to elaborate intelligent monitors that can take the environmental context into account. We show in this paper some main abilities of BN that can help in the elaboration of fault detection isolation and recovery (FDIR) modules. One of the main difficulty with the BN model is generally to elaborate these ones according to the case of study. Then, we propose some automatic generation techniques from failure mode and effects analysis (FMEA)-like tables using the pattern design approach. Once defined, these modules have to operate online for autonomous vehicles. In a second part, we propose a design methodology to embed the real-time and non-intrusive implementations of the BN modules using FPGA-SoC support. We show that the FPGA implementation can offer an interesting speed-up with very limited energy cost. Lastly, we show how these BN modules can be incorporated into the decision-making model for the mission planning of unmanned aerial vehicles (UAVs). We illustrate the integration by means of two models: the Decision Network model that is a straightforward extension of the BN model, and the BFM model that is an extension of the Markov Decision Process (MDP) decision-making model incorporating a BN. We illustrate the different proposals with realistic examples and show that the hybrid implementation on FPGA-SoC can offer some benefits.