Actually, at the San Diego Comic Con, the show writers/creators were asked about the Scootaloo situation, and they said something along of the lines of "just because her parents haven't been seen doesn't mean she's an orphan".
By the way, I LOVE the colors, the warm & cool greys, and lighting effects! It all works together to give a real sense of place and environment, even with a cartoony style. (And I love the style in general, by the way. )
We've had a bit of weather like that down here in Florida as of late (minus rainbow-colored flying ponies, of course), as we're into the rainy season and these things tend to blow in quickly and then sometimes just rush on again over the peninsula -- so it's not that unusual to be walking across the street and the sun is shining down at an angle, and you can see a patch of blue sky, yet there are plenty of dark grey clouds to go around, and rain is coming down where you are.