High-level synthesis (HLS) tools have provided significant productivity enhancements to the design flow of digital systems in recent years, resulting in highly-optimized circuits, in terms of area and latency. Given the evolution of hardware attacks, which can render them vulnerable, it is essential to consider security as a significant aspect of the HLS design flow. Yet the need to evaluate a huge number of functionally equivalent de-signs of the HLS design space challenges hardware security evaluation methods (e.g., fault injection - FI campaigns). In this work, we propose an evaluation methodology of hardware security properties of HLS-produced designs using state-of-the-art Graph Neural Network (GNN) approaches that achieves significant speedup and better scalability than typical evaluation methods (such as FI). We demonstrate the proposed methodology on a Double Modular Redundancy (DMR) coun-termeasure applied on an AES SBox implementation, en-hanced by diversifying the redundant modules through HLS directives. The experimental results show that GNNs can be efficiently trained to predict important hardware security met-rics concerning fault attacks (e.g., critical and detection error rates), by using regression. The proposed method predicts the fault vulnerability metrics of the HLS-based designs with high R-squared scores and achieves huge speedup compared to fault injection once the training of the GNN is completed.