Optical networks constitute the backbone of contemporary communication infrastructures, supporting massive bandwidth, low-latency services, and high levels of scalability across core, metro, and access domains. As these systems evolve toward elastic, software-defined, and multi-domain architectures, their exposure to sophisticated security threats increases significantly. This paper provides a comprehensive survey of vulnerabilities and countermeasures in modern optical networks, spanning the physical, control, and cross-layer dimensions. We analyze major architectures—including WDM, TDM, PON, EON, and IP-over-WDM—and examine how their structural properties shape their security posture. A threat taxonomy is presented covering physical-layer attacks such as fiber tapping, optical jamming, crosstalk exploitation, and signal injection; control-plane risks including spoofing, malicious signaling, and SDN manipulation; and broader cross-layer attack vectors. We review state-of-the-art defense mechanisms, including physical-layer security (PLS), spectrum randomization, chaotic optical coding, device-level authentication, survivability techniques, intelligent monitoring, and quantum-secure solutions such as QKD. By integrating insights from recent experimental and operational studies, the survey highlights emerging challenges and identifies open problems related to secure orchestration, multi-tenant environments, and quantum-era resilience. The objective is to guide researchers, engineers, and network operators toward robust and future-proof security strategies for next-generation optical infrastructures.