for the iPhone you may be right. Not for the touch, however. An app that's only available part of the time isn't always useful. For example a finance app, a gas tracking app, a notepad, shopping list, games, etc etc etc...
If you can only access them from one place people will always prefer native apps. Whether or not everyone hacks their iPod to allow native apps is another issue...
Basically native apps will be prefered indefinitely until apple releases a real web sdk.