I want my application to be unsearchable from the App Store. I would like that only those users who sign in to my web site and then click the link of my iPhone application on ap
Your application will be found when they search for the name of the app or your name. There's no special option in iTunes Connect to hide your app.
While your application will be found when searched for, as long as it's not installed in large numbers, it won't show up in the top 50 lists. Which kind of is the same.
Tip: don't specify any keywords when registering your app, as these will improve the "searchability".
Edit: you might want to implement some kind of authentication in your app, so users who do have installed your app need to register first, before they can actually use it. Relying on your app not being found, isn't very "clean".