Evil Queen: What’d you tell them?
Rumpelstiltskin: The truth! That nothing can stop the darkness. Except, of course, their unborn child. You see, no matter how powerful, all curses can be broken. Their child is the key. Of course, the curse has to be enacted first.
It only stands to reason that Regina would at least suspect who Emma is. She knows that Snow and Charming’s child is the key to breaking the curse. She knows nothing has changed in SB for years and years. She knows that 28 years after Snow’s baby is born a 28-year-old shows up in town and things start to change. Regina can’t be so dense as to not put the pieces together by now.
It is a good question why she didn’t just get rid of Emma as soon as she realized. If she worried about hurting Henry, she could have just made Emma disappear and said she left town. I think she has to be biding her time because she doesn’t know how much effect Emma has had on the curse already. Her mere presence has started the curse crumbling, so maybe she worries that once it starts to fall apart, there is no stopping it. Maybe she thinks she has to defeat Emma in a more decisive way. If she realizes who Henry’s grandparents are, she might worry that Henry also has some ability to destroy the curse, since he doesn’t seem to be affected by it. Maybe she is just in some MAJOR denial and refuses to think about who Emma is because it means she is doomed. In any case, I hope this question is addressed sooner rather than later. I bet they confirm that Regina knows before the season is over.