Maritime Autonomous Surface Ships (MASS) have emerged as a promising solution to enhance navigational safety, operational efficiency, and long-term cost effectiveness. However, their reliable deployment requires rigorous verification and validation (V\&V) under various environmental conditions, including extreme and safety-critical scenarios. This paper presents an enhanced virtual simulation framework to support the V\&V of MASS in realistic maritime environments, with particular emphasis on the influence of weather and bathymetry on autonomous navigation performance. The framework incorporates a high-fidelity environmental modeling suite capable of simulating adverse weather conditions such as rain, fog, and wave dynamics. The key factors that affect weather, such as rain and visibility, are parameterized to affect sea-state characteristics, perception, and sensing systems, resulting in position and velocity uncertainty, reduced visibility, and degraded situational awareness. Furthermore, high-resolution bathymetric data from major U.S. ports are integrated to enable depth-aware navigation, grounding prevention capabilities, and evaluation of vessel controllability in shallow or confined waterways. The proposed framework offers extensive configurability, enabling systematic testing in a wide spectrum of maritime conditions, including scenarios that are impractical or unsafe to replicate in real-world trials, thus supporting the V\&V of MASS.