so you can activate Disappearing messages on whatsapp for 24 hours, 7 days, or 90 days after they’re sent.
these messages are disappearing only for the user or get it deleted from whatsapp servers to?
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Nobody knows, your guess is as good as ours. 
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Messages are never stored unless your contact is offline. When they’re online, the message arrives and it gets deleted from the server. It is only ever stored encrypted.
In the end, you have to trust the app of the contact that they remove the message.
(Online in the sense of “they have internet”)