It seems that ioncube leaves intact those comments by default, according to their documentation:
3.15.3 Omitting Documentation Comments [ --no-doc-comments ] Documentation comments are comments with the following syntax: /** My code comment */ These comments are exposed by the PHP 5 reflection API, and are preserved by the PHP 5 Encoder by default. In order to omit these documentation comments from encoded files specify the --no-doc-comments option.