Welcome, Machiavelli! Your excellent question shows that you took good care in choosing your nom de plume.
A guess is that the "dark fact" that Hagen dares not ask is: What role does the Don intend for Michael when he returns to America from Sicily? A clue is found a bit earlier in the passage that you cited:
The Don asks Hagen if he disapproves of anything the Don did that day. Hagen says no, but he adds that he doesn't believe the Don is not interested in why Sonny was killed, or in avenging him. It's "not true to [the Don's] nature." Hagen says the Don has "constructed a magnificent riddle." The Don seems enormously satisfied that Hagen has made that analysis.
I infer from this passage that, while the Don gave his word not to avenge Sonny, he didn't constrict Michael. To that point, Hagen might have viewed Michael's murder of Solozzo and McCluskey as a necessary expedient to save the Don's life. Now Hagen's dreaded question is: Does the Don intend for Michael to take over the family? And will Michael--his little brother, the college boy--now act in cold blood to avenge Sonny?