Yes, I think that's his point too. But if you believe that the little details of biology emerge from the underlying physics, then maybe you only need to code the fundamental rules and can have all the rest automatically.
My simpler point is that Kurzweil's not taking a useful measure for the size of the system we're solving. (By the way, he plays the same kind of trick on his audience when he's pointing out there are only a few billion neurons in the brain - as if that were the only level of complexity in the brain).
No, common English use of "it's hard" means something completely different from CS "hard". CS hard means NP-complete which to English translates as impossible. Impossible because of well understood mathematical reasons.
Quantum computers may solve it, indeed real life protein folding may have quantum computer-like properties.
My current project is a search engine for protein chain geometry. We only have ~20% of the known proteins in our database because the data on the other 80% isn't accurate enough to be useful.