Bastion speaks pure machine code, so did Bastion select the name to have it be translated or did Torbjorn or perhaps another member of the Lindholm family give her her a name? I don’t know the Northern Cardinal species, I presume only the female of the species makes nests.
I can only guess the name comes from how the she flies around Bastion like how the moon Ganymede orbits Jupiter.
It’s a shame more isn’t seen of Ganymede, it would be nice if she could occasionally return to visit bastion in combat, maybe it could be a kind of subtle passive, Ganymede would only appear if there are no one is around Bastion and will fly off as soon as anyone approaches, whether friendly or hostile. Ganymede wouldn’t appear immediately once Bastion was alone, it’d be a random thing but Ganymede would always fly off if there was someone near or within line of sight.