Flood hazard maps are essential for protection and emergency plans, yet their probabilistic application is constrained by the computational cost of numerical models. Deep learning surrogates can provide orders of magnitude faster predictions, but their use for uncertainty quantification in realistic settings and their ability to incorporate hydraulic structures remain largely unexplored. Studying deep learning surrogates for probabilistic flood maps is non-trivial because of the lack of reference ground-truth data that might lead to misleading confidence in predictions. Moreover, hydraulic structures are challenging to include due to their generally unidimensional nature. In this work, we investigate the use of deep learning surrogates for realistic, large-scale flood simulations in case studies with hydraulic structures, under diverse boundary conditions. To this end, we employ the multi-scale hydraulic graph neural network (mSWE-GNN) that enjoys transferability to different boundary conditions and locations and whose graph-based architecture allows to represent structures such as canals, underpasses, and elevated elements as inputs. To address the lack of reference ground-truth data, we further introduce the average relative mass error (ARME), a mass-conservation-based criterion that helps identify physically plausible simulations. We apply the model on dike ring 41 in the Netherlands, generating probabilistic flood maps that account for uncertainties in breach location and breach outflow hydrographs. The model was trained on 30 simulations, generated with Delft3D, and evaluated against unseen benchmark simulations from the Dutch national flood catalogue, achieving a critical success index (CSI) of 73.6 % while running 10,000 times faster than the numerical simulator. The proposed ARME is negatively correlated with the CSI, with a Pearson correlation coefficient of <span>−</span>0.7, making it a useful indicator of simulation plausibility when evaluating unseen case studies. We obtained probabilistic flood maps by running 10,000 different flooding scenarios on a computational mesh of 180,000 cells in approximately 10 hours with about half of the simulations classified as plausible based on the mass-conservation check. This framework offers a practical tool for rapid probabilistic flood hazard assessment and a way to prioritize detailed physical simulations, supporting more efficient and robust flood risk management.