I know that they definitely both do appear in the original Ruby and Sapphire, and in Emerald. They can clearly be witnessed battling in the center of the city (not sure about RS, but in Emerald, they could be seen upon entering the city.)
As for the new ones, I'm pretty sure that's a no. not once did I ever see Kyogre being depicted in the game other than Secret Base battles. I looked for this during a playthrough and I don't recall Kyogre ever existing other than its name.
If someone can prove I'm wrong, go ahead and hide this. I'm about 85/100 sure on this one.