Data-driven generative design (DDGD) methods utilize deep neural networks to create novel designs based on existing data. The structure-aware DDGD method can handle complex geometries and automate the assembly of separate components into systems, showing promise in facilitating creative designs. However, determining the appropriate vectorized design representation (VDR) to evaluate 3D shapes generated from the structure-aware DDGD model remains largely unexplored. To that end, we conducted a comparative analysis of surrogate models’ performance in predicting the engineering performance of 3D shapes using VDRs from two sources: the trained latent space of structure-aware DDGD models encoding structural and geometric information and an embedding method encoding only geometric information. We conducted two case studies: one involving 3D car models focusing on drag coefficients and the other involving 3D aircraft models considering both drag and lift coefficients. Our results demonstrate that using latent vectors as VDRs can significantly deteriorate surrogate models’ predictions. Moreover, increasing the dimensionality of the VDRs in the embedding method may not necessarily improve the prediction, especially when the VDRs contain more information irrelevant to the engineering performance. Therefore, when selecting VDRs for surrogate modeling, the latent vectors obtained from training structure-aware DDGD models must be used with caution, although they are more accessible once training is complete. The underlying physics associated with the engineering performance should be paid attention. This paper provides empirical evidence for the effectiveness of different types of VDRs of structure-aware DDGD for surrogate modeling, thus facilitating the construction of better surrogate models for AI-generated designs.