Will any of the weapons be pilot-controlled?

That's the same with the AI turrets. We'll be able to slave some of them to the pilot, but not all of them. Read the Shipyard posts.

As far as the ship's state in 3.3, because we don't have AI, server blades, slaving, stuff like that, in 3.3 will anything be pilot-controlled?

You will need buddies.