You actually reminded me to do something I've been meaning to do for a while - ask about if Pokemon-ex and Pokemon EX are treated the same way, or differently.
I'm going to ask Chrisbo directly, and see what he says. Then I'll get back to you.
Edit: I was notified by [member]Stratus[/member] that they were different; I asked where he got the source and he said it was on Pokegym. I snooped around and found these two threads:
http://pokegym.net/forums/showthread.php?t=160780
http://pokegym.net/forums/showthread.php?t=160181
So I guess Desert Ruins won't affect Shaymin EX.
I'll still be waiting for Chrisbo's response, but odds are he's going to say the same thing.