Depends on the site. For example, the forum manager can see deleted posts. And, in fact, the whole world can read all non-deleted posts.
But messages in Whatsapp are encrypted and nobody but the adressee can read them.
What do you mean with "server manager? Since you post in the ISP-forum, let me tell you that the ISP can't see messages on devices of the sender or receiver, but in principle, can see everything that passes his webserver, unless you use https: protocol or the equivalent for ftp. That's true for e-mails also, e-mails aren't encrypted.
But, then, using the word "deleted" doesn't make sense. Since your ISP doesn't store them there is no possibility for anybody to "delete" it there.
Maybe make your question somewhat clearer?
I would like to know if the server manager can read messages from users.
If yes, the deleted messages can be read too?