This study contributes to the advancement of vehicle occupancy estimation in Automated Guideway Transit (AGT) systems using Wi-Fi probe requests and deep learning models. We propose a comprehensive framework for evaluating various approaches to occupancy estimation, particularly in the context of MAC address randomization. While many methods proposed in the literature claim effectiveness in simpler experimental settings, our research reveals that those methods are unreliable in the complex environment of AGT systems. Specifically, techniques for handling randomized MAC addresses and distinguishing between passenger and non-passenger data do not perform well in AGT systems. Despite challenges in tracking individual devices, our study demonstrates that accurate occupancy estimation using Wi-Fi probe requests remains feasible. A pilot study conducted on the Miami-Dade Metromover, an AGT system characterized by frequent stops, significant occupancy fluctuations, and absence of fare collection devices, provides a robust testing ground for the framework. Additionally, our findings show that deep learning models significantly outperform machine learning models in this context. The insights from this study can significantly enhance decision-making for transit agencies to optimize operations and elevate service quality.