The increasing demand for reliance on autonomous systems in maritime operations, particularly in vessel mooring and cargo handling, has raised significant concerns regarding operational safety and security. As these operations become more advanced, the risks associated with cyber vulnerabilities and their potential to affect safety are escalating. This paper focuses on the selection and justification of methodologies for a risk assessment framework that will be developed within the EC-funded project SEAMLESS for autonomous mooring and cargo handling systems. The main objective of this framework will be to identify, evaluate and mitigate both cybersecurity risks and hazardous scenarios, ensuring these systems are safe and secure by design. In addition, the paper highlights possible cascading effects of hazardous incidents within these operations considering the critical component interdependencies in both operations.