Derpy is our shoutout to the bronies. It's been this way since halfway through season 1. I'd love to know what other examples of background ponies in season 2 you think are direct shoutouts to fans, because I don't think we are defining things the same way which may be cause for some confusion. Derpy is the only background pony whose status has changed, and I honestly don't foresee any other background pony getting the same treatment.
Do you see any differences between a shoutout and an easter egg? For me, I consider Derpy as something for the fans, whereas if I put a silly green unicorn in the background (something I've been doing since before it became a hit with the fans) I see it more as an easter egg, something I do for fun, regardless of if bronies were around or not, and it's something I will continue to do. You'll find these sorts of things in a lot of cartoons, it's just something artists do for fun when it's appropriate.
I think I need to coin a new term: 'The Brony Goggle Effect'. You can probably see where I'm going with this... it's pretty much where a brony chooses to interpret things seen in the show as directly targeted at them even when there is really no easter egg or shoutout in the first place. As an example, if 2 random background ponies happen to be in a scene together, people with 'brony goggles' may interpret it as the pair sharing a romantic relationship and being a shoutout instead of the far more likely truth that they are simply part of a crowd meant to make Ponyville feel like a lively town instead of a barren wasteland with no other ponies but the main cast. "OMG, if we freeze-frame this scene just right, it looks they're making lovey-dovey eyes! What? They're just blinking? Nah, that would actually make sense, and we can't have that."
The way we make the show hasn't changed from season 1 to 2, and won't change going from season 2 to 3. Our goal is still to make an awesome cartoon for girls that their parents can enjoy watching with them, and if parents can enjoy the show, there's no reason other adults can't too. Really it just comes down to us wanting to make the show good, and good is something anyone can like.