That was actually a pretty nice scene, suggesting she could tell his right hand wasn't so natural. I can also see where your other theory would come from considering she has asked him a couple of times if he's really Shinichi, as if she knew, as well, that there are people who aren't what they seem to be. However, her own arm can't be a parasyte since the parasytes can sense each other's presence. Even if her parasyte would be completely uncooperative, which is unlikely since it would also be trying to survive, Migi would have told Shinichi about it in any case.