JBrony
[@Inkan1969](/images/635041#comment_2497451)
I think magic alters their bodies so their ears are replaced with fully functioning pony ears on the tops of their head, as well as likely slightly altering their head and skulls to make this work. It's the same with Rainbow how she suddenly gains wings, yet they are not only full flesh and blood wings capable of flying, but she instantly knows how to use them.
In short, their human ears magically vanish to make room for pony ears!
Plus, it also rearranges various lobes in their brains to make the auditory system closer to the tops of their heads.
Note this screencap from “Forgotten Friendship” for example (look closely at Pinkie Pie, specifically the area where her hair was lifted up: 
I think magic alters their bodies so their ears are replaced with fully functioning pony ears on the tops of their head, as well as likely slightly altering their head and skulls to make this work. It's the same with Rainbow how she suddenly gains wings, yet they are not only full flesh and blood wings capable of flying, but she instantly knows how to use them.
In short, their human ears magically vanish to make room for pony ears!
Plus, it also rearranges various lobes in their brains to make the auditory system closer to the tops of their heads.
Note this screencap from “Forgotten Friendship” for example (look closely at Pinkie Pie, specifically the area where her hair was lifted up: 