From everything I've heard, the deck that won Canada didn't run Yanmega....though, I'm not 100% on this as I wasn't there.
And, you aren't really taking the meta game into account. Yanmega is steamrolling right now, which makes donphan a pretty bad play, especially paired with the fact that Kingdra has seen a lot of play and one pretty well. Just about anything OHKO's Zekrom, so its weakness is moot. Donphan 3HKO's Magnezone while getting OHKO'ed in return, so it really has no place as a deck, only as a tech. Zekrom can handle one Donphan. Just about everything else in the format is easy enough to KO by other attackers and while Donphan does set up quick, it doesn't have a high damage output and damages its own bench. I'm not saying its horrible, I'm saying you can get away with not teching against it.