Open-source software (OSS) dependencies are a dominant component of modern software code bases. Using proven and well-tested OSS components lets developers reduce development time and cost while improving quality. However, heavy reliance on open-source software also introduces significant security risks, including the incorporation of known vulnerabilities into the codebase. To mitigate these risks, metadata-based dependency scanners, which are lightweight and fast, and code-centric scanners, which enable the detection of modified dependencies hidden from metadata-based approaches, have been developed. In this paper, we present Unshade, a hybrid approach towards dependency scanning in Java that combines the efficiency of metadata-based scanning with the ability to detect modified dependencies of code-centric approaches. Unshade first augments a Java project's software bill of materials (SBOM) by identifying modified and hidden dependencies via a bytecode-based fingerprinting mechanism. This augmented SBOM is then passed to a metadata-based vulnerability scanner to identify known vulnerabilities in both declared and newly revealed dependencies. Leveraging Unshade's high scalability, we conducted a large-scale study of the 1,808 most popular open-source Java Maven projects on GitHub. The results show that nearly 50% of these projects contain at least one modified, hidden dependency associated with a known vulnerability. On average, each affected project includes more than eight such hidden vulnerable dependencies, all missed by traditional metadata-based scanners. Overall, Unshade identified 7,712 unique CVEs in hidden dependencies that would remain undetected when relying on metadata-based scanning alone.