Removing app from iOS app store and notifying users that the app is no longer supported
However you want to notify your users is up to you.  Doing so is not a technical question but more of a choice of whatever's easier/faster/convenient for you.  If you have the ability and desire to notify users before you shut down, my suggestion is to do that.  Users might not be happy with losing use of the app but at least you'll have the respect of knowing that you gave everyone ample notice.  

There is no customary procedure because every app and user-base is different.  I would also recommend contacting your users with every method you have available.  If you can popup a message, do that; if you can send an email, do that; if you can post to Twitter/Facebook, do that.  There's no way to overcommunicate an app shutdown.

The only thing I would recommend against is creating an app update that just shows a message about the app shutting down.  Users will feel tricked and you'll have a mess and lost of confidence.  

If users can still use your app without any further updates from you or without your backend services, let them use it.  Once you remove the app from the App Store, users will not be able to restore it from backup; once it's gone, it's gone.

UPDATE: Per discussion in the comments to this answer, there appears to be a difference between restores done via iCloud and iTunes. @Hitechcomputergeek points out iTunes can back up actual apps, while iCloud only backs up their data and re-downloads the app itself from the App Store (like if you had first downloaded it).