You might recall that when Apple first released the iPhone there was no app store and no way to install apps on the phone. The only way to add functionality to the phone was by running apps within the Mobile Safari browser, although iOS did, and still does, provide a way to add a bookmark to the home screen as an icon so that you could start the web app in the same way as all other apps.
While Apple later added support for native apps on the iPhone and iPod Touch, there are still many web apps available, and Apple includes a bookmark to a catalog of them in Mobile Safari. iOS 4.3 includes improvements to the software used by web apps so that they run more than two times faster than on the previous version. It turns out, however, that web apps that are saved to the home screen do not gain the same performance improvement.
Ars Technica has confirmed the performance difference and provides an explanation for why it exists. Without getting too technical (you can read the Ars Technica’s article for all the details), the improvement that Apple made only works for code that starts to run within Mobile Safari. When you save an app to the home screen, it runs within the iOS Springboard and it does not have the ability to run the code in its optimized form and that is for security reasons.
The bottom line is that if you use web apps on an iPhone, iPod Touch, or iPad, to get the best performance, save them as bookmarks in Mobile Safari and start them from in the browser rather than from the home screen.