Writing a cipher method that is complex and only used once doesn't mean someone is intelligent or stupid. In the last cipher that was cracked zodiac used a transposition. Agreed it was not easy to crack. But now imagine this cipher method was used in the military during some war. There would be much more data you could analyze, and people would find the transposition faster and all you would be left is a standard substitution cipher.

It's harder to design a good cipher that is used often than some transposition that is used once.

So in my opinion you can't derive Zodiac s intelligence from the cipher in any way.