I'm a game designer. Anyone who thinks that this is a sign of some flat Earth-believing game designers is just grabbing for straws. There are three major reasons why a video game world appears to be flat.
1. The game world does not correspond to the real world. As far as you know, Wind Waker takes place on an infinitely large sphere. Or on a cube. Especially in aesthetically simple games like Wind Waker, adherence to reality is not only unnecessary, but usually avoided.
2. It's simpler. Even in basic terms. To draw a quadrilateral, you need four vertices, which create four lines and one face. To make even the simplest possible hemisphere, half of an 8-sided die, you need five vertices, creating eight lines and four faces. A moderately nice looking hemisphere at that scale requires hundreds of vertices to look acceptable. And if you only wanted to render a curved horizon, that would be even more work, as you would have to distort a plane after it has already been rendered. In short, it's easier for everyone if you just have a quad.
3. Gravity. In games, gravity works by increasing the vertical velocity of things in the down direction. In a flat world, gravity always exists in the same direction. In a round world, gravity points towards the center of the mass. When you have variable gravity, you will end up with variable collision. Zelda floor collision is very simple. You are either touching ground or you aren't. To make it acceptable in 'round' terms, you would need to rework your collision engine to make the character conform to the rounded terrain. This goes back to the 'it's simpler' point. There's just no need to put all that extra work into making the game round.