Apple introduced iCloud in 2011; before that, users had to rely on iTunes to store your data in your computer. Wi-Fi Sync and iCloud were yet to be materialized.
The apps on your iDevices eat up space on your computer; but on the other hand, you had an advantage of restoring those apps even though the apps were removed from AppStore.
Coming to the current situation – when you perform restore action of your data, note that the apps are stored remotely; no matter you take an iCloud or iTunes backup. The iCloud backup will store your personal app data while the app itself will be stored on AppStore server.
This is because of App Thinning, a smart move from iOS 9. This allocation system allows you to create a universal app for iPhone and iPad. If the iPhone you own contains only half of the app, you won't be able to take full back-up to your computer using iTunes, therefore the iPhone has to depend on the cloud.
If something happens to your iCloud, you may have to lose hope of restoration of third-party apps. You should also be prepared to lose apps you own; because these apps are no more stored on AppStore and you cannot restore from a backup. In this situation, you can follow some solutions given below.
How to Fix Missing Apps Issue on your iPhone 6s/6s Plus
Check Your Wi-Fi Connection
There is no comparison between your cellular data and Wi-Fi internet; if you restore apps using your mobile data, you will be pissed off by its speed. Even if you restore the apps, they will not be doing anything. You should better check your Wi-Fi network. If you are not using a strong Wi-Fi connection, you apps might hang.
Jump Your App to Top
Jumping your iPhone apps to the top of download queue may help you. Check whether your third-party apps are visible or not; now tap on the app icon to bring it to the top of download series. Though this solution doesn't give you positive result every time, it can serve the purpose if you are stuck in any situation. If your app is not seen at all (I mean if it is missing), this method will not help you.
If the problem persists, delete the app in question and download it again. Long press the app and a delete icon (x) will appear on the app. Delete the app and re-install it from the app store.
Go for the Force Restart
Force Restart can solve many issues on your iPhone, which in this case, could be stuck on iCloud; or maybe it has stopped its functions because of other issues. You can restart the entire procedure by rebooting your iPhone; press the power and home buttons simultaneously until you see the Apple logo on iPhone screen.
Go to the Purchased Section
An erroneous backup process will delete the app completely. This time, either you can go for phone restoration (provided you have all the time to do this) or re-download that single app in question. But you need to re-download the app from the Purchased section: AppStore → Updates → Purchased.
Ideally, this should save your app's data once you re-download. If the backup was in error, you may lose the data.