I was aware of this glitch. I am not 100% sure, but I believe the reason is the degree of effect the Ditto glitch has on the game. Its effects extend beyond the examples you've quoted, and it was determined to be detrimental to the game, so it was banned. From what I've read, this seems reasonable, and I recall it being hinted at before as being the reason, but I personally don't recall it being directly stated. There is no reason to ban the Shaymin/Darkrai glitch.
Then please, instead of saying 'You can get it through a glitch', list every reason why that glitch is permissable and others aren't.
There was a lengthy discussion on this topic several months ago. The conclusion was that we do not "know" we're getting Arceus simply because it's in the pokedex, because we've inevitably gotten every other pokemon, or for any other reason, nor would that knowledge have any bearing on whether or not hacking Arceus is permissible. Why would it?
We don't know we're getting Shaymin either. Probably, but not 100% sure. I mean those people could change their minds completely. And I brought up hacking because I see absolutely no difference between the Surf glitch used to get Shaymin and walk-through-walls/hacking Oak's Letter to get Shaymin.
If something is possible in-game without the aid of an unauthorized, external device, then it is allowed (provided, of course, that there is not sufficient reason to do otherwise). If otherwise, then it is not allowed. Others are free to operate by whatever definitions they wish, but that does not necessitate consequence or change here.
I was under the impression that Smogon doesn't allow anything obtained by such a glitch to be used in a tournament, and that hardly anyone considers glitch Shaymin legal. And again, there's hardly any difference between glitching to get Shaymin and hacking to get it. The creators are in opposition to both and if you showed up at a tournament with a Shaymin obtained through a glitch they would turn you away. If you didn't care what the creators think then there's no reason to be opposed to getting it either way.