She's likely a life fiber infused human like Ryuuko and Ragyo, although she still lost her eye, so at the time 6 months before she may have not been. But, she is human, and alien in some way.
It looks like we have an answer (As of episode 20).
The reason her eye didn't regenerate may be due to something along the lines of life fibers not being able to perfectly repair everything. Or maybe if you cut it the right way with the scissor blade a body part won't regenerate.
There's also the possibility that her eye is fine and she's just covering it up for some reason.
Oh man, that'd definitely be interesting; Ryuuko could probably use the scissor blade to actually kill Ragyo and maybe even free her own body from the life fibers, then.
Still, the fact that Ragyo/Nui haven't mentioned (I doubt they haven't noticed) the fact that Nui's eye hasn't regenerated is a bit weird. Either they're trying to keep it under wraps, or, like you said, she's lying about the eye being gone to trick Ryuuko, or something along those lines.