Industry 4.0 technologies have the potential to transform logistics by enabling smarter, more autonomous warehouse systems. However, Shuttle-Based Storage and Retrieval Systems (SBSRS) still rely largely on centralized or hierarchical control architectures, limiting their adaptability, scalability and responsiveness. While existing research has focused on optimizing control policies within these conventional frameworks, the architectural layer itself remains underexplored. This study investigates the impact of control architectures on SBSRS performance by comparing a conventional hierarchical model with a hybrid control architecture that introduces local autonomy and inter-shuttle communication. A hybrid Discrete-Event and Agent-Based Simulation model was developed to evaluate both architectures, using a tier-captive SBSRS inspired by Vanderlande’s ADAPTO system. System Performance was assessed under varying system sizes and shuttle densities using throughput, normalized efficiency, scalability and robustness as key performance indicators. The results show that the hybrid architecture consistently outperforms the centralized approach in throughput, especially in large scale system, with up to 36\% throughput gain, up to 68\% efficiency gain (normalized throughput), improved scalability and reduced variability. These findings suggest that hybrid control offers a promising path for designing adaptive, Industry 4.0-ready SBSRS. The study contributes a conceptual design and simulation-based comparison to guide future control architecture development.