Well, unfortunately X knows all, and frankly he doesn't see Darko as a dark god. All gods are both good and evil, their motivations are their own, and their powers unique to their purposes. Secrets are both malicious and benign, so is death, shadows and other things. Hence reading between the lines of the interaction, though X mocked Darko's powers over death (as things persist after death), it also served as a warning to him to consider his place as the Lord of Oblivion is to come. 

As for reasons as to why X would know of Darko's intent, just as Darko has control over the forces of Death and when a life ends, X controls the realm of knowledge. He is Truth and sees through the veil of deception. Nothing can hide itself from X, for it is he who hides things. Not by shadows, nor by deception, but rather by striking out memory of events as they happen, such that to the rest of the universe it never did. 

What he does not know does not exist, or perhaps Should not exist, and even then things which should not exist are listed in his books, and thus he knows of them and their existence.