First, can The Hundred see Kellhus' death, there in the Golden Room? Aren't they blind to Golgotterath and everything inside it? Does Yatwer even know he's dead?
From the conversation between Kellhus and the Mutilated, it seems the Gods can see
him just fine. They just can't see where he stands. I agree that this is the weakest part of my theory, though.
But here's something to think about. The Consult are not content to just sit in Golgotterath until they die. Which implies that merely being there doesn't completely hide you from the Gods, at least after you've died. So I'm pretty sure Yatwer knows that Kellhus dies in there, even if she can't see the events that immediately surround it.
Also, I'm pretty sure merely being soulless doesn't render one invisible in the sight of The Hundred. Animals are soulless and they don't appear to be invisible to the gods. I think the gods can see sranc, skin spies, etc. just fine.
It's possible the Gods can see them, but they don't attribute any agency to them. They are just machines as far as the Gods are concerned.
To Yatwer, the only visible souls/agencies involved with Kellhus' death are Sorweel and Esmenet. They both intended death to Kellhus, and Kellhus died in proximity to them, and with no other souls/agencies around that Yatwer could perceive. Hence she intuits (because she cannot reason) that they killed him. She sees the outcome and the intentions, and fills in the missing details of the causal chain in an intuitive and rather dim manner.