There is no way that he noticed anything about the change in Itachi's tone or voice because he literally was quite deaf, his somewhat-good ear now ringing loud enough to drown any bit of sound he could have otherwise picked up. He had to read the other's lips and strain to his right ear to even try to understand what was being said. "Yeah. It's in the job description."

And wait, what? Watching him die? So it was a threat. Or, TARDIS was real. The lack of response, however, was probably Shisui's way of telling the other that it was okay to check his ears as long as he wasn't going to put a bullet in them. It didn't look like this version of Itachi carried a gun, though.

Shisui raises an eyebrow at what he makes out with the lip reading. "We're supposed to be on the same team. We don't fight." A beat. "We bicker." Like an old married couple, but you didn't hear him say that~