Maybe a value could be set in the config file, e.g., $cfg['maxSuhosinLength'] = 1000; and the warning only be triggered when a $_POST/GET possibly will reach that limit?
Then could someone please check whether
ini_set('suhosin.request.max_vars', $GLOBALS['cfg']['maxSuhosinLength']);
has the desired effect (I don't have access to a suhosin protected box):
Jürgen