The reason may be that the Emperor and the Baron Harkonnen have different goals in the conflict.
The Baron wants his enemy, all of them down to the last soldier, dead. His motivation is one of burning revenge:
"The Harkonnens won't rest until they're dead or my Duke destroyed.
The Baron cannot forget that Leto is a cousin of the royal blood--no
matter what the distance--while the Harkonnen titles came out of the
CHOAM pocketbook. But the poison in him, deep in his mind, is the
knowledge that an Atreides had a Harkonnen banished for cowardice
after, the Battle of Corrin."
And that quote brings me to the next point. The Duke Leto and the Emperor were distant relatives. He very likely did not want any harm to come to a member of his family. The Emperor's reason for engaging in the conflict wasn't personal, it was to ensure supremacy. Hawat explained it to Baron Harkonnen:
"The Padishah Emperor turned against House Atreides because the Duke's
Warmasters Gurney Halleck and Duncan Idaho had trained a fighting
force -- a small fighting force -- to within a hair as good as the
Sardaukar. Some of them were even better.
The Emperor was involved only as a political necessity. Most likely he was hoping that once Duke Leto's armies were smashed, he would retire to Tupile:
TUPILE: so-called "sanctuary planet" (probably several planets) for
defeated Houses of the Imperium. Location(s) known only to the Guild
and maintained inviolate under the Guild Peace.
Remember that there were strict rules in place to keep royalty safe during wartime, too.
DICTUM FAMILIA: that rule of the Great Convention which prohibits the
slaying of a royal person or member of a Great House by informal
treachery. The rule sets up the formal outline and limits the means of
The Emperor had every right to think that Duke Leto would survive the conflict. The Baron, however, had other plans:
Others in like circumstances have become renegade Houses, taking
family atomics and shields and fleeing beyond the Imperium."
"The Duke's too proud a man for that," the Baron said.
"It is a possibility," Piter said. "The ultimate effect for us would
be the same, however."
"No, it would not!" the Baron growled. "I must have him dead and his
And the death of Duke Leto sent the Emperor into a rage:
When my father, the Padishah Emperor, heard of Duke Leto's death and
the manner of it, he went into such a rage as we had never before
Which brings us to the Truthsayer. The Baron had to engineer deaths for his opponents, but do so in such a way as to look like you were playing inside the rules, and to be able to speak the truth in front of the Emperor's Truthsayer, and not offend the Emperor. It was a very delicate thing. That's why they had to do all the circumlocution. It was noticed by Count Fenring:
"The Emperor cannot be unhappy about the death of the concubine and
the boy," the Baron said. "They fled into the desert. There was a
"Yes, there were so many convenient accidents," the Count agreed.
So the Emperor definitely suspects, but cannot prove the Baron went against his wishes and purposefully had the Atreides killed. The Baron's plan was a success in that regard.