after the don makes the peace, he meets with hagen alone and the book says that hagen still didnt know the whole story and that as he pieced the story together there was still one thing that was not spoken of, something the pointed to a day of reckoning in the future. what specifically does this refer to? does it refer to the killing of the heads of the five families, to knowing that carlo was going to have to be taken out, or to something else entirely? also, why was it that hagen wasnt allowed to know about these things? thanks in advance for responses.

It was for the reasons you stated. I think the reason that Hagen was never involved in the planning of any crimes was because he was the Family's lawyer. If they were to ever get into serious legal trouble, ala the Senate Hearings, it would be best to have Hagen defending the Family instead of being a co-defendant.

Notice that the Don tells Hagen that he made the peace to insure Michael's safety, and that Hagen's number-one priority is to get Michael home safely. That's all he says about Michael in that scene. But the "one dark fact, that he had not dared to mention...that pointed to a day of reckoning..." was: what was Michael's role to be in the Family when he returned?
Nothing that went before indicated that the Don would make Michael his successor--in fact,prior to the Sollozzo/McCluskey shootings, the Don wanted Michael to have nothing directly to do with the Family business. So, Hagen must have been wondering what Michael's role would be when he returned. Also, Hagen told the Don that he couldn't believe that the Don wanted to let Sonny's murder rest: the Don had constructed a "magnificent riddle" for him. I think Hagen must have been wondering if the Don intended that Michael would carry out vengeance for Sonny.