Dynamic Hybrid Pallet Warehouses (DHPWs) are a novel class of automated warehouses, combining the advantages of shuttle-based and stacker crane-based warehouses by using shuttles for transport in the horizontal direction and stacker cranes for the vertical connection of the tiers. The literature for conventional shuttle-based and stacker crane-based warehouses shows that the design influences the performance considerably. In this paper, we investigate the influence of the main design elements that characterize the performance of DHPWs through discrete element simulations for different types of DHPWs and in different operating modes. The design elements under investigation are the configuration of the transfer buffers, the location of the input/output area, the number of levels and the size of the shuttle fleet.