Are there Get/Set methods for addressing commerce line_items and order object properties?
What you're doing is correct for Commerce 1.x.  Drupal 7 just uses stdClass objects for entities, no methods. Fortunately Commerce 1.x isn't seeing any significant changes - any time we make an API change it will be heavily noted in the change log of a new release. Additionally, Commerce 2.x on Drupal 8 is actually able to use robust classes for entities, so the future is brighter.