First, skip to the part when Obi-wan finished watching the security recording in the Jedi Temple. After he is done he talks to Yoda about how to destroying the Sith. Obi-Wan refers to Palpatine as the Emperor in this quote.

"Send me to kill the Emperor, I will not kill Anikan."

How does he know that he is the Emperor? An Emperor is the leader of an empire and Obi-Wan wasn't there when that meeting was held announcing the formation of the galactic empire. Obi-Wan may know he is the Sith Lord, but then he would either call him the Sith Lord or Darth Sideous.