First rewatch. Seems pretty well established that the consensus is that Stewy is a smart guy. Maybe not Logan/Mattson level but certainly not on the level as the siblings.
Stewy’s last interaction with Kendall before he backs out of the deal is Kendall jonesing for drugs to the point where Stewy looks borderline uncomfortable. He knows Ken’s background with addiction and how unhinged he can become, and then he presumably doesn’t see Kendall for multiple hours as the waiter storyline unfolds.
The next morning there are (true) rumors circulating about a dead waiter. The same waiter that briefly interacted with Logan near Kendall and Stewy. Then Ken backs out the deal and Stewy even asks Kendall point blank, “how did he (Logan) get to you?”
I understand some secrets are better kept for the sake of the plot but there is no way you can convince me Stewy couldn’t put all of that together and figure out Kendall had something to do with the dead waiter.