It's one realistic thing they put in
tWW: Stamina. Link is a 10 year old kid! How far do you honestly think he could have swum? Only Olympic athletes (and Zelda aquatic life forms) could swim island to island. And if you're talking about diving, there really wouldn't be any use. Old Hyrule is hundreds of feet beneath the surface, there's no way he would have been able to survive down there (unless he had some sort of mermaid suite like the Link had in
OoA).
Then you have the monsters to think about. Even if Link could swim from one isle to another, there wouldn't be a way to defend himself from the onslaught of attacks from the octorocks, and other monsters of the deep.
With that said, nothing could have been done in
PH. They made you drown so it would be an obstacle you'd have to work your way around (just like Link not being able to jump small gaps in earlier games). For example there was a temple where he had to lower and raise the water level. If Link could swim, there wouldn't have been a challenge...or a real purpose to the whole (simple) puzzle.
-BGS