But even if they are identical surely the computer can figure out "hey, there are two pokemon exactly the same with the same id number and the same hidden values, there isn't supposed to be, this has been cloned"
a more sophisticated version of my first post should work.
There's still a small almost impossible chance that they can have the same EVs, it's possible, I've tried. However, we can keep arguing about this forever, nothing going to change either way.
The system might not work at all if Wi-Fi isn't hosted by a server, but instead just each others games emitting a signal. The system could be used as a patch, but here's the problem, they're not going to patch it via internet. This is likely as when the D/P gltches were discovered, I never saw the option of receiving the patch via Wi-Fi, if even possible. It had to be fixed at select stores or by sending it to Nintendo directly.
I'm sure Wi-Fi would be flooded by online events as much as cloned GBA Event Pokemon, also, cloning is still possible in D/P, via trading flaws. >_>