I have seen various discussions about this rule, but not quite in the exact same context, so I am unsure if that could be merged with an existing issue:

I upgraded to eslint-plugin-import v2.31.0, which officially supports ESLint V9. Enabling the import/no-unused-modules with the existing unusedExports option results in the ESLint CLI not recognizing the eslint.config.js unless there's a .eslintrc file next to it (the .eslintrc file can be empty; it just ignores it).

Oops! Something went wrong! :(

ESLint: 9.11.1

ESLint couldn't find a configuration file. To set up a configuration file for this project, please run:

    npm init @eslint/config@latest

ESLint looked for configuration files in <project rootDir> and its ancestors. If it found none, it then looked in your home directory.

If you think you already have a configuration file or if you need more help, please stop by the ESLint Discord server: https://eslint.org/chat

As long as the .eslintrc exists, the rule works as expected.