commerce_line_item VS field_data_commerce_line_items
My answer concerns the structural and not the semantic difference between the two.

The table field_data_commerce_line_items corresponds to a standard drupal field. On the other hand commerce_line_item is a table that is managed by one of the modules in the commerce module family.

The table field_config_instance describes the relationships between drupal fields (which are actually tables such as field_data_commerce_line_items) and higher level entity types (i.e. node) and bundles (i.e. content type) that reference them.