No, no 3DS emulator currently exists. As far as we know, no one has even fully cracked the Nintendo 3DS, meaning development for an emulator likely hasn't even started (or if it has, it hasn't advanced much). Emulation can only be done once we fully understand how the Nintendo 3DS works, but this time around there's a whole lot of encryption to sift through. I wouldn't expect development to start for at least a few years.
And no, Pokemon X and Y are Nintendo 3DS games, and hence they are not playable on a DS emulator like DeSmuMe.