Is there a reliable way via php cli or a system command whether or not httpd, or a particular site, has suphp enabled?

Run this in root cli:

/usr/local/cpanel/bin/rebuild_phpconf --current

you can also know this by looking into your php info page.

<?php
system('id');
?>

Granted, it assumes Linux and that the whoami command is installed but
it should work. If it doesn't come back with the username of the
script owner, it isn't working (in the simplest case).

<?php
system('id');
?>

Granted, it assumes Linux and that the whoami command is installed but
it should work. If it doesn't come back with the username of the
script owner, it isn't working (in the simplest case).

That would only prove that either open_basedir is set, or "system" has been added to the "disable_functions" option.

If, in addition, a phpinfo() output indicates that the Server API is CGI, then it's a safe assumption that SuPHP may be in use.