According to tech site The Register, however, when you launch a bookmarked web app from your home screen rather than launching it from inside Safari, "it runs roughly two to two and a half times slower than it does in the browser."
Web apps launched from the home screen suffer from other diminished capabilities as well, including problems storing data offline. It's kind of frustrating news, and conspiracy theories abound ("Apple's crippling web apps so you have to buy native apps through the App Store!"), but right now the only takeaway is this: For now, if you're a big mobile web app user, you'll want to open your favourite web apps after you've launched Safari — and avoid launching the web apps directly from the App links you've added to your home screen. We'd imagine Apple will address this problem — intentional or not — in a future release.
Apple handcuffs 'open' web apps on iPhone home screen [The Register]