Unfortunately, I think it might be true. Picked up the Wii version in the hopes it'd look stellar, but it really does look like it might be a 640x480 image stretched to 16:9. Even though it's going through HDMI, there's an overall blurry sheen to it that I'm not noticing on the GameCube version through component (on the Wii), and details seem less defined. When I move in close to models and textures and go into first-person mode, jaggies don't appear to be as crisp on the Wii version (being played on the Wii U) when I switch back and forth between inputs. When I stretch the GameCube version to 16:9, it has a similar kind of look; and when I squeeze the Wii version to 4:3, it looks more crisp like the GameCube version, but obviously distorted since there's a wider field of view.
It could just be my eyes playing tricks on me since I've already gotten it into my head that the Wii Twilight Princess may not be natively 16:9, but it really does appear to be the case. When I can get right up to Ilia's face and see sharper outlines around her model and around the eyes (more jaggies), and texture on her face that appears more detailed, I think it's safe to say the Wii version really is a 4:3 image that proportionately looks 16:9 when viewed as such, but is in reality the exact same resolution as the GameCube game and not a proper widescreen image.
Actually, now that I'm looking up details on the resolution of the Wii, it sounds like its max res is 640x480 but when set to widescreen, it's essentially a 16:9 image in a 4:3 resolution. So no Wii games are true 16:9—not in the sense I'm thinking of it anyway, where the resolution would be 854x480 (or whatever slightly lower res the Wii would actually use if it were "true 16:9"). Meaning, widescreen Wii games don't have a pixel aspect ratio of 1:1 but something wider.
I...guess I expected and always assumed something more out of the Wii. If it's really just a 640x480 resolution morphed to 16:9, I'm a little saddened. And I threw $20 down the shitter if that's the case. D: