The problem with Amy, is that we know where she is almost 24 hours a day, she is literally almost always working (poor girl, kind of be funny if she only took those jobs to be close to Veronica), so, unless she can be in more than one place at a time...
Mom definitely knows more than she is letting on, and the way she reacted negatively to her, could mean any number of things, whether she knows who it is or not, but her getting up for work so early makes it hard for it to be her if one of her powers isn't 'never having to sleep'. Her room is usually locked, so it's possible if the no sleep thing can be accounted for, and I can think of a few ways, but Occam's Razor...
Emma, on the other hand, doesn't have to be at work until almost noon. She moved around a lot and has a sketchy past, etc. Almost everything about her screams 'secret identity'.