Actually, he thinks it had something to do with Lelouch and geass, not that he necessarily killed her.
He himself is confused. On the one hand, if he killed Euphie, then it's not a huge stretch of the imagination for him to kill Shirley, as well. But to Suzaku, geassing and killing Euphie makes no sense (go watch Turn 8 again), considering what he knows of Lelouch and how Lelouch ordered him to "Live!" Killing Shirley would similarly make no sense.