Templates are never actually run through PHP that way, no matter the extension. NNF uses DOM templating (http://camendesign.com/dom_templating), that just happens to have HTML as a base.
It is currently impossible to mix PHP and HTML for the template.
Instead you can use the
`theme_custom` method to add extra actions to the DOM templating if you want to mix in extra stuff. See: https://github.com/Kroc/NoNonsenseForum/blob/master/themes/greyscale/theme.php#L73