Sub folders and how to namespace classes
@Clive is correct.

The namespace is always Drupal\{module_name}. Where that module lives is irrelevant (as long as it is somewhere where Drupal can find it). That namespace always points to $path_to_module/src.

It would not possibly work in any other way. Different sites have modules in a different structure and different places, but the same code has to work no matter where.