They wanted it like that. Maybe, they made it a way so you can tell if someone hacs or not. If you see someone with a shiny zekrom/reshiram, you know for a fact that they hack and you shouldn't trade with them. That's just a theory and truely just game freak knows.
GameFreak shiny locked them, so you wouldn't waste your time by trying to catch them, and begin to play the game instead.
It's just a theory.
I think that GameFreak wanted people to try and divide up the awesomeness of strong Pokemon (Zekrom/Reshiram) and awesome Shiny Pokemon (any other Pokemon). Besides, would you rather have a weak shiny Pokemon or a super strong none-shiny Pokemon?