He definitely notices how unpleasant the smile is. He doesn't like it. Though the rest of Hythlodaeus' demeanor, his tone and actions, Emet-Selch can't particularly say he hates it. Even if he is rather confused at the moment.

"Pretty? Average at best, what in the world are you going on about?" He squints at Hythlodaeus, trying to stop the two of them from walking. "You're angry. What's happened? I was not intending to fulfill any quota requirements with that gentleman if that's what you think."