There's an upside to using them too: You can send tracking data back to your app through the Apple App Store 'black box' allowing you to track where your users come from. Use the 'app-argument' meta tag variable and put your tracking info within the URL.
While that's neat, I feel like the kind of developer who makes a fullscreen pop-up ad for their app every time you visit the site simply doesn't care enough to do this thing.
Unrelatedly, I feel like I saw a presentation about security flaws with these a little while back? (Not a danger to people using them on their site, but rather they could be used to sniff various information about the user's device)