So far I've only seen boys named Emery though???
Let's think about this rationally.
1) You've only seen boys named Emery. Because it's a boy's name. You've probably also only seen boys named Dave, Kevin, and Sebastian- are you adding them to your name list too?
2) I really don't get naming a girl a boy's name. It might work out for her if she's gorgeous and popular. But on the off chance she's normal or *gasp* god forbid, overweight, nerdy, or acne-ridden, it's going to be miserable for her. And as much as we all like to imagine our daughters being the head cheerleader, even famous supermodels complain of ugly-duckling high school stages. It seems really cruel to give your child a masculine name on top of that.
3) your other daughter has a lovely, classic, feminine name. Is Emery going to think you wanted a boy and were stuck with her? Or is she always going to be jealous of her beautiful sister who got the "good" name?