A lot of mobile optimised web sites display App Store links on the top of the page.
How to block this annoying ads? I already run and ad blocker for iOS.
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I’m afraid the answer is you can’t block them, at least not through a setting in iOS or a Content Blocker extension for Safari. There are patches available for jailbroken devices though.
These ads are shown through the “Smart App Banners” feature of Safari. As far as I know, there is no setting in iOS to turn them off. Because of the way Safari Content Blocker extensions work, I also don’t think they can block the HTML tag that tells Safari to display the ad.
At least Safari does seem to remember that you don’t want to see an ad for a particular app (or on a particular site, I’m not sure) if you close the banner using the “⨯” button on the left.