"Who told you that the agreement has already been signed?"
I wonder whether we should observe the sequence of tenses rule and make it "Who told you that the agreement had already been signed?"
The sequence of tenses is also called backshift. It is better to regard it as a common usage rather than a rule to be applied in all cases. As The Oxford Dictionary of English Grammar (p45) states in its entry on backshift:
... backshift (sometimes known as the sequence of tense rule) is not automatic.
The Cambridge Dictionary of English Grammar (p318) has this extract in its entry on sequence of tenses:
In classical Latin the tense of the verb in the main clause influenced that of the verb in the following subordinate clause, especially in reported speech. This principle was taken up by traditional grammarians in modern English.
In formal writing and reporting, the sequence of tenses is usually practiced, whereas in everyday discourse it is not necessarily observed.
The CDEG gives examples in which observing the sequence of tenses rule would either change the meaning of the sentence or would render it ambiguous. It then states:
In such cases, the pragmatics of communication take over to ensure that the tense sequence works to support the intended meaning.
As @Janus Bahs Jacquet points out in his comment, the use of the present tense in the reported clause (has already been signed) indicates to the listener that the report is currently in a signed state. The present tense is used to emphasise present relevance.
The backshifted version, using the past perfect tense (had already been signed), places more emphasis on the time point of the signing; namely, before the reporting of it.
There have been numerous questions about backshifting on this site. Here is one that contains an answer with further extracts from reference grammars on the issue: