In development... well, I guess GameFreak decided to remake R/S as far back as a month or two after the release of HG/SS. Maybe it was planned for the fifth generation, but pushed back when Gen. V turned out to be a short one (which wouldn't have been long afterwards anyway). Or perhaps they knew from the start that Gen. V would be short, and decided to wait for Gen. VI. Creative input for the remake of Hoenn would have been a more or less continuous process, with the most important decisions taken somewhere in X/Y's late development (this would be anything requiring backwards capability, or at least addressing content that wouldn't be compatible, so the appropriate barriers could be put in place [such as the mechanisms preventing the Griseous Orb to be traded from Platinum to D/P]). Once X/Y was finished, they would already have most of the framework for ORAS as well. All Pokémon models (with animations), an engine to run it all on, overworld models, et cetera. The layout of the region and the main story is also finished already, and wouldn't need any major overhauls. Creating ORAS once X/Y is finished should be a trivial matter. They may very well not have started with it until X/Y had shipped, since most of the work was done already.Sorry if you've answered this before but since you seem like the person which the best grasp on this, how long do you reckon these games have been in development for then?
Also, couldn't they just be trying to be sneaky if they do add a patch? Keep the games hidden until they announce it? Nintendo must've known the games would get hacked
As for keeping stuff hidden until they announce it... I really doubt it. If so, they would have kept Hoopa, Diancie, Volcanion and all that hidden too. It makes no sense to half-ass it by having some of the stuff you plan to release hidden in the code, but not all of it. It's kind of an "all or nothing" scenario, doing it halfway would practically be asking for bugs to happen.
Also, I doubt we will see a "GBA Sounds" in ORAS. The difference in music style between G/S and HG/SS was significant enough to justify it (going from 16-bit beeps to actual instruments), but between R/S and ORAS it's less dramatic. The music wouldn't be that much different with worse instruments either way.