I dont want to beat a dead horse, and I can't imagine I'm thr first person to harp on this. I propose an alternate view on why Cortana suddenly has clothes.
The presence or absence of garments does not automatically imply anything about a body at all, in my opinion. Just bc shes suddenly wearing clothes in Halo 5 does not imply she was 'naked' earlier, or that she now has features to hide.
Garments have many purposes, not just to hide a body. There are 2 other reasons: to shield the wearer from the environment, and to communicate something about the wearer. As Cortana's form is not physical and cannot interact with physical environments as we understand it, that is unlikely to be the cause for her to suddenly be wearing clothes.
Instead, I think its likely she's trying to communicate something about herself. We can identify firefighters by their uniform- clothes communicate something about the internal. I'm willing to bet she wanted to change something about her outward appearance to signal an internal change. She chose a very specific garment for a very specific reason.
Her new clothes are harsh and unyielding. Other than some interesting geometric patterns, there's very little decoration on her suit. It's functional. Thats it. She's signaling that she's here to get work done and that she's not to be trifled to with.
Sure, IRL, the developers might have suddenly wanted to cover her to get the T rating. However lore wise, I think it's a very reasonable change.
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