I don't see what would prevent them from having said data? Especially when 3DS carts are like 10 times the biggest DS carts minimum...
Black City and White Forest are both in both BW2 games. Different maps with their own NPCs events and all, accessed by keys. Same for the golem caves, where the entrance is simply made to lead you into a different room.
There would be a few more for an integrated Emerald...the Magma HQ I guess. But quite a lot more NPCs and events sure.
Far from a serious problem though since RS and E share everything that matters.
I mean, think of it this way. They had RS. Then they adjusted it to create E. This would be the same, just instead of replacing anything, they add the data and make a key switch between that.