Right but Suhosin also allows you to configure the limit variables if necessary. The default is 200 which should be fine.
I doubt that PHPMyAdmin uses more than 200 request variables. If they do, the application is badly designed.
Other than that Suhosin does not filter variables silently. You can send filtered actions to a log.
All this is done finally since PHP 5.3.9, so if this is a problem with Suhosin, it is a problem with PHP too now.