Since Shaymin can only be obtained via event normally (if I recall correctly,) but you can catch it without obtaining the wondercard via tweaking, will it have the fateful encounter flag needed to get the gracidea flower if caught via tweaking; or do I need the wondercard to activate it? Same goes for Darkrai
A Shaymin caught at the Flower Paradise in Pokémon Platinum will be a fateful encounter Pokémon.
I'm pretty sure it's the same in DP, but I'll hide this answer if you're still skeptical. source
You can get shaymin and darkrai with the tweaking glitch, but the Pokemon you get from tweaking won't trigger any other events. So nothing will happen if you show shaymin to the gardacia person, and she won't give you the gardacia flower unless you have the wonder card.