I think the hookshot has been overused. It has appeared in almost every game since LttP yet it has an interesting position of being one of the few pieces of technology found in Hyrule that no one complains about.
I have assumed that the whip would be the replacement in SS. And that it's function would be very similar to the grappling hook of WW. It could be a stunning weapon, give Link the capability to swing and hang from ledges, bind enemies, or remove items from enemies. like the grappling hook. Plus the Wii controls could give the player a lot more variation in how you use it other than the very typical hookshot point and shoot. With the right controls a whip could be a lot more useful.
Off the top of my head I can think of applications like stealing an enemy weapon out of it's hand, swinging travel in every forest or temple ceiling, rupee stealing from enemies, grabbing items from across the room, grabbing rocks or pots and swinging them into enemies, swinging enemies into enemies, binding an enemy arm so they cannot swing a sword at Link, grabbing and moving blocks in temples, setting off traps in a distance. If the whip is capable of half this then it will be more useful than any hookshot.
Link has explored more temples than Indiana Jones, and kill more monsters than any Belmont. A whip sounds like a perfect addition that requires no magitech to explain away like a hookshot. And it can still easily fit into the medieval setting of Zelda, more than the boomerang.