The Giant hinted that she used Smite Evil on Belkar, after which she knew he was evil, the same way she knew Roy wasn't evil after she tried Smite Evil on him. Detecting Evil on Belkar now would be redundant. And that also means that she was confident enough Belkar was evil, once she no longer felt obligated to give Roy's word on the matter any weight, to use Smite Evil on him. The Order is lucky she bothered to chain him up instead of gutting him, once she'd determined for certain that, yes, he's evil. (Whether it's good luck or bad luck is another matter.)