parsing submodules seems to be not working

The only common thing I found is they all are located in a sub-folder below the main module.

Right now composer installated sub-modules are only found within following directory structure: <MODULE_NAME>/modules/<SUB_MOBULE_NAME>.
An example that works: web/modules/contrib/PARAGRAPHS/modules/PARAGRAPHS_DEMO for the paragraphs module.

Can you please share the paths and the way how to install these modules/extensions? That way it can be debugged.

E.g. the folder structure for
modules/contrib/bamboo_twig
modules/contrib/bamboo_twig/bamboo_twig_config/bamboo_twig_config.info.yml
modules/contrib/bamboo_twig/bamboo_twig_i18n/bamboo_twig_i18n.info.yml
..

I just use composer require ... for each contrib module.
e.g. composer require drupal/bamboo_twig

I have no idea how they are installed.
What are you looking for exactly?

I checked the bamboo twig module locally ($ composer require drupal/bamboo_twig), but I cannot reproduce the problem.

The error you see is triggered here:

// Remove "drupal/" prefix for Drupal modules, because that breaks
// the table output in the report.
if (!str_starts_with($packageName, 'drupal/')) {
  $error_message = "Could not parse Composer information for module '" . $module->getName() . "'";
  throw new UnusedModulesException($error_message);
}

Do you have anything special with the composer setup? Symlinks or complete git checkout for each modules?

I tested with views_aggregator & computed_field modules and cannot reproduce the issue described in the description. I can see information about both modules and their submodules.