Shuttle-based storage and retrieval systems (SBS/RS) are an important part of automated warehouses. SBS/RS are often used if throughput demand is high. SBS/RS can have significant advantages compared to crane-based automated storage and retrieval systems (AS/RS) with regard to throughput, energy efficiency and flexibility, depending on the application. Therefore, in the last ten years, the market for SBS/RS has grown considerably. Research of SBS/RS has not been as thorough as in the case of AS/RS. In particular, the development and investigation of the storage management policies class-based storage, sequencing of retrieval requests and warehouse reorganization and the resulting throughput increases and reductions in energy consumption during their application have considerable potential. This paper demonstrates the potential for throughput improvement in the application of these storage management policies. A simulation model is used to determine the throughput. The results show that significant optimization of the throughput is achieved by the application of the presented storage management policies.