From what was written in the new EU so far, it seems to me the fact that the Emperor is a Sith and a Dark Side user is a secret that only very few know. Some high ranking officials and officers probably know or at least strongly suspect, but your average galactic citizen has no idea who Palpatine really is or even how he really looks like now. The official image of the Emperor is how he looked before his face melted. And besides, not many people in the galaxy probably know what Sith is anyway. That said, I think the Inquisitors definitely know the Emperor is a Sith.