You know, it's interesting that Sonic's environmental themes are pretty much gone at this point, when it's never been more important to be concerned about them.
Fantastic right? The pro environment messages of the late 80s/early 90s were all for nothing. I think part of why that messaging in general was moved away from though is because that more shamed individuals into like recycling and such which on paper sounds great, but when it’s really 4 companies contributing to like 60% of all polluting, you’re paper straw or putting your Coke can in the right bin isn’t going to do much in the long run (hell you could even put the can in the right bin, but it still might not get recycled). And really what the hell are kids going to do about logging, drilling, fracking, and big oil?
I think the main reason they've been wanting to avoid showing animals popping out of Badniks recently was so you don't question where they go. Like in the Adventure games we see Sonic take them into the Chao Garden to feed them to the water babies but you can't really take the time to show that in a comicbook.
Keep in mind that Robotnik had already pretty much moved away from Flickies (and small animals in general, since there's more than the birds) in robots since Sonic Heroes, a 2003 game. The line would make no sense even without Sonic the Hedgehog (IDW Comics), assuming it still being 'set' in the game continuity. Still, this is the IDW thread, not the continuity nor Sonic Prime thread.
Regardless of how "canon" Prime is, any commentary it makes on lore minutiae should really not be taken as gospel.
Theory on why no flickies: Spoiler Maybe they didn't have flickies because they plan on blowing up or otherwise destroying the whole city and didn't want to suggest the casualties or deal with having to safely move them out.
