I think she knows Noble are not HER Spartans, as in her journal she mentions her suspicions of someone using her research for an inferior version of her S-II program, and she even goes as far as to hypothesize that Noble may be from a parallel program (such as Javelin) that has piggy-backed on her work from the last three decades. She even goes as far to mention in her journal that Mendez, a major part of the S-II program is still missing, whereabouts unknown to her.
But for her to extrapolate from this data that Mendez and someone (Ackerson) have created a new generation of Spartan IIIs, on Onyx of all places, and having done so without her attention is a stretch, even for Halsey's mind, hence her surprise at finding a company of S-IIIs at Onyx and a "dead" Spartan. I mean, even if she hadn't just escaped Reach and then had to hi-jack a ship to reach Onyx I don't think she would have had time to piece this together.
It just goes to show ONI's capabilities of compartmentilisation of sensitive information, being able to hide such information from Halsey such as this, when she is able to find damn near anything that ONI does.
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