In the past years MLP was nominated for the Emmy, yes it didn't won, but perhaps was either the competion was hard or the songs were not so good "Find a Pet" and "The Pony Everypony should know". Also I really don't think that the Emmy are complete ignorants at comparation of other academies (coff Oscars).
Now talking about the song's nomination.
It is totally deserved, and also to win, from all the songs of season 5, thry choose the correct one, The Magic Inside is inspirational, sentimental and beautiful, I have no more words to describe this song.
To be honest, I heard the other songs competing against The Magic Inside and the only main competion is True Bromance from All Hail King Julien, and probably We are gonna space die of Turbo Fast, the other two are meh, for pre scholars.
I hope MLP wins this, they totally deserve it, this can shut up many people judging that MLP is for girls, a bad show, etc.
Let's just wait for the ceremony.