You may have accidentally moved it, there is a search option which may help you find it.
Go to your PC enter - Lanette's PC - Organise Boxes - Press Y - Set Pokemon to "Mew"
This will then blackout all of your Pokemon that aren't Mew making it easier to find.
If that doesn't work maybe you traded it or put in the GTS.
Aside from that I don't really know, if it was hacked in there may be a few ways it could have disappeared.
