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Blatant hacks aren't allowed through Pokebank, so it's not like we were gonna get a Wondertomb in XY anyway.
>b-but the 3DS will be hacked!
IF that ever happens, and that's a big if, I doubt it will be as easy to do as DS hacking. 3DS patches everything with each update; if we hack the GTS Game Freak can develop a patch as well. Don't act like they don't know what we've done to 4th and 5th gen. I'm willing to bet DNS won't be involved in the new GTS, and in that case, we are fucked (considering we even figure out how Pokemon data is generated in the first place).
The good news is that you can still run Wondertomb in PWT and Battle Subway and Black Tower and Battle Frontier (watch out for Fire Fang though). Don't worry about it.