Wasn't there a UNIT man in TCI? He didn't seem to be keen on the idea of contacting Torchwood, IIRC. It's possible they have a very cold relationship with each other, in which case UNIT might not feel the need to divulge the identity of one of their alien consultants. So Torchwood would only know the Doctor as a dangerous man and Harriet Jones certainly won't be correcting that opinion any time soon.