Once Palpatine says that he knows the nature of the dark side, Anakin stops and steps ahead of him. He doesn’t ask “You know the dark side?”, he just kind of goes on guard and glares at him, so you can infer that he already has an idea of where it’s going. He doesn’t ignite his lightsaber yet. He lets Palps talk until “…save your wife” then he ignites his lightsaber without asking “what did you say?”

So he doesn’t automatically assume Palpatine is a Sith Lord, but once he hears about the dark side, he stops verbally engaging with him until there’s more “proof” of Palps’ sith lordiness, which is like one and two more sentences, I guess.

…

And since we’re on the topic of this scene, something else I did with it was I cut the “more and more I get feeling that I’m being excluded from the council…”

I changed the lines a bit so it now goes “I wish I knew… But I know there are things about the force that they’re not telling me - (re-insert) I’m being excluded from the council.” Anakin is supposed to be more confident all around in my cut, I think him making a direct assertion about what’s going on, and not what he kind of thinks/feels is going on better serves that.