Using these in an email is probably going to be in a workplace. The basic meaning of all 3 is that the documents (pieces of paper, or electronic) have been given from someone to someone else already, at the time the sentence is being typed.
The documents are already handed over and The documents have already been handed over mean basically the same thing, that at some point in the past the documents were handed over.
The last one is slightly different, it is a tense usually known as the pluperfect. What this basically means is that it occurred in the past before another past action. Usually this is used to compare two things that both happened in the past, to show that one happened earlier than the other. You wouldn't really use the last one on its own like that, as it sounds a little weird. You would say something like "The documents had already been handed over when I got to work this morning." The documents were handed over in the past, AND you got to work in the past, but the documents being handed over happened first out of those two things. You can also make this form from the first sentence by changing it from "the documents are already handed over" to "the documents were already handed over"
I hope this helps!