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Theres some stuff, like Blaze Black/Volt White, but not much in terms of really in-depth hacks. The programming for the games has gotten significantly more complex with each gen, and all of gen 5's additions, particularly graphically, make it more difficult to work with from what I understand.
I think it will be gotten to eventually, but there's also an element that if you are going to be doing a complex romhack, you want to probably do it in a more solo-creator friendly environment, and so gen 3's simpler sprites and programming makes it a prime destination, and then the work from those romhacks increases the knowledge of hacking there, which then makes it easier, etc
