Locke was ONI agent, but he wasn't undercover, he was Acquisitions Specialist.
I think your problem is that you think that undercover ONI agents will look somehow special. They don't.
They look like regular humans, they don't stand out at all.
Take Maya Sankar for an example, she was for many years undercover working on the Insurrectionists and their cells. She was FERO and no one, no one knew she was deep down ONI, something they wanted to fight against, while they were believing and following FERO.
Seriously - you'll NEVER recognize an ONI agent, unless they want you to see them. They could be disguised even as a homeless person just not to loose their cover.