I think that a lot is control circuitry, like the bits that regulate digestion or body temperature. I don't see any reason that for a superintelligence these could not be consciously controlled. The main reason we have so many unconscious processes and heuristics in our brains is to limit the total power consumption, as that was super important back in the days when food was scarce. If power consumption becomes less important, you could do more and better thinking.