I'm afraid that setting only takes effect for languages that scan for all files in your repository (JavaScript, Python, Ruby (see https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/customizing-code-scanning#specifying-directories-to-scan)). Java analysis works by following along with your build process, so if you want to exclude particular files from analysis you need to specify a build process that does not build those files.

Another approach is to use the advanced-security/filter-sarif Action to filter out results before reporting them.