We analyze the utilization of publish-subscribe protocols in IoT and Fog Computing and challenges around security configuration, performance, and qualitative characteristics. Such problems with security configuration lead to significant disruptions and high operation costs. Yet, These issues can be prevented by selecting the appropriate transmission technology for each configuration, considering the variations in sizing, installation, sensor profile, distribution, security, networking, and locality. This work aims to present a comparative qualitative and quantitative analysis around diverse configurations, focusing on Smart Agriculture's scenario and specifically the case of fish-farming. As result, we applied a data generation workbench to create datasets of relevant research data and compared the results in terms of performance, resource utilization, security, and resilience. Also, we provide a qualitative analysis of use case scenarios for the quantitative data produced. As a contribution, this robust analysis provides a blueprint to decision support for Fog Computing engineers analyzing the best protocol to apply in various configurations.