I could not find a way of running the phpunit tests for subplugins.
My workaround was doing some custom step in the GHA, but it would be nice if this could be integrated into the moodle-plugin-ci "phpunit" command directly or a new command phpunit-subplugins or similar could be created.
Here my GHA configuration for documentation purposes and everyone that stumbles over this issue in the meantime:
https://github.com/bycs-lp/moodle-local_ai_manager/blob/main/.github/workflows/ci.yml