Will the apps share cloud saves and some in-game purchases from Android device to iPad?

Solution 1:

Will I be able to keep all in-game purchases for all games?

This will very much depend on the app and how in-game purchases are handled. Usually, if you have an account for that app they can be transferred.

Will I be able to cross-save (like I cant carry my iPad everywhere, so I will keep Clash of Clans in the Android device as well)?

Yes, this does work with Clash of Clans and many other apps. However, this also may depend on the exact app.

Do I need to pay Netflix, Amazon prime subscription again?

No, they are linked to an e-mail address and you can use the same subscription on multiple devices although there is a downloads (i.e. you can't download unlimited hours of content onto your devices) limit.

What is the difference between iTunes and App Store, and which one is used to buy apps and stuff?

These days for most users only the AppStore is important, this is where you download and search apps, start updates and can see family shared apps. iTunes is now mainly used to buy music. It used to be Apples main online marketplace for digital media, but for the last years apple has split e.g. films into a separate app (tv).

Solution 2:

It depends on the app, so there is no general answer for this. Things like Netflix etc which are designed to be used on several devices (you can watch Netflix with the same account from Android, PC, Mac, iOS etc) will work as expected. For games it may be different depending on how the account management works in-game.

PS: The App Store is for Apps, the iTunes Store is for music.