The whole "A Roy sound file and a Ryu sound files being in an unrelated patch" honestly felt like too big of a mistake to actually have been made. Nintendo is aware that the encryption on the 3DS has been broken to the moon and back, and wouldn't they want someone as big as Ryu to be, I dunno, a surprise? I'm sticking to the belief that at the very least Roy is a red herring (getting the rights to the Ryu sound file just to be LOL NOPE might be not worth the effort, but it's not out of the question) until proven wrong.
If Roy is a red herring, I think that it's very likely that another FE character will be put in in his place, and in my eyes Kamui is the most likely candidate for that.
In fact, now that I think about it, Ryu's files being real would make Roy being a red herring even more convincing. Let's say they reveal both new fighters at E3. They start with Ryu. Yeah whoo hooo, childhood nostagia and whatnot. They immediately follow it up with another new fighter trailer. At this point, everyone is expecting Roy, since Ryu happened to be the real deal. In the trailer, Marth, Ike, Lucina, and Robin are all fighting. It's four FE characters, so it has to be a FE character being revealed, and who else would it be besides Roy? Then, suddenly there's fire, and the FE crew jumps back. A FE character with fire, so it HAS to be Roy! As the flames start to die down, we can see the Marth, Ike, Lucina, and Robin's surprised expression, before the camera does a 180, revealing Dragon!Female Kamui to be the source of the flames, who quickly reverts to her human form.
"I'm sorry, were you expecting someone else?"
Then the splash art, and then the moveset part of the trailer.
If they wanted to go even further, halfway through the moveset trailer, Roy appears, and it becomes a Roy reveal trailer.
Even the red herring was a red herring!
...maybe I'm overthinking it. Yeah, probably.
tl;dr, I wouldn't say it's a 0% chance, but really can't bring myself to believe that it's all that high