Right now it is not clear if this is a bug or if Apple is intentionally doing it to push for native apps. However, an unnamed developer is of the view that Apple is intentionally crippling web apps so that developers develop native apps.
Apple is basically using subtle defects to make web apps appear to be low quality – even when they claim HTML5 is a fully supported platform.
Unlike native apps which have to be developed separately for each platforms, web apps has the advantage that they can be developed once and can be run in Android, iOS and any other platform that supports HTML5. More importantly, web apps do not have to pass through Apple's App Store - thus eliminating the fee that Apple would have taken if it were a native app.
So, Apple has some financial gains to make by forcing developers to make native apps instead of web apps. However, there is also indication that point to suggests that this is a bug and Apple did not do this intentionally. This issue affects iOS's UIWebView API as well. UIWebView is used by native apps to offer web contents inside native apps. As Apple already takes their cut from native apps, there is no point for them to intentionally cripple performance in the native apps as well.
On top of this speed issue, web apps launched from the home screen in iOS are also crippled in two key aspects. They cannot use the HTML5 Application Cache and they are rendered with the old "synchronous mode" instead of the new "asynchronous mode". The inability to use cache means that the web apps cannot run offline. The cache access was apparently cut off in iOS 4.2. And the fact that the web apps are rendered with synchronous mode means that they do not look quite as good as it would have had asynchronous mode been used.
I am no Apple fan and generally do not like many of the things they do. But, in this case, I do not think that Apple is doing this intentionally. In my opinion, there is no conspiracy here and this is just a bug.
What about you? Do you think that this is just a bug? Or is this a conspiracy by Apple to force developers to develop native apps? Let us know your thoughts.