Why is this shady? If I intentionally click on a link to an app, why would I not want that link to open the App Store?
I'm seeing this practice increasing and spreading. It must be effective.
I've seen it on some big web properties. The other day I was browsing the Guardian and boom, iTunes opened. If spent some time afterwards on my PC and Fiddler duplicating the views using a faked user agent to watch the redirects and cookies. It is slyly done. Normally it only happens once per session. They drop a cookie so that they don't persistently annoy the user, just once in a while.