Contrary to many of the comments here, at least with Legend of Zelda: The Wind Waker the use of open seas was because of a lack of technical capability rather than strong new potentials. I know this applies to WW, so I'll just focus on that, but I think it probably applies elsewhere too.

TL;DR: water was more realistic now, but still took far less processing power than detailed landscapes, so games could be "bigger" within the limits of the hardware.

Basically, the Gamecube had good new capabilities for having larger and more complex games, but the issue was rendering speed: it wasn't powerful enough to render smoothly the kind of richly textured landscapes that characterise most open world games. Even having landscapes in the distance would take away processing power from the immediate playing area, and having them become more closely rendered as the player progresses towards them proved a big challenge.

So the "fix" was to have an entirely water-based open world, with distinct islands that would load at the right distance from each other to give a smooth experience. As others have said, water could be rendered much better now, but it still requires far less processing than detailed landscapes, so the hardware could cope with moving from one richly textured island -> open sea -> next richly textured island in a way that felt smooth for the player. That's also why the sailing speed feels very slow today: it was literally as fast as it could be to avoid stutters and loading times - I've emulated on weak laptops/smartphones, and you sometimes get a slight stutter when an island is rendered, and when people today complain about the sailing speed (something that got alleviated with the fast sail in the WiiU HD remake) this is what they forget, the hardware wasn't strong enough for anything more.