This take may be a bit hot, but I actually think paper and pen is already the optimal maxima for thinking—not for retrieval, mind you, but for helping us produce new thoughts. Zettelkasten (at least the way Luhmann used it) is meant for this purpose—it is not a system for storing information and retrieving it but rather for supporting the creation of new connections.
The computer aided tools are suboptimal for this because they lack the good constrains of paper (severely limiting the search space) and the good features (seamless ability to incorporate a variety of representational modes, text, image, equation, with zero overhead, and the ability to organize things freely in space). As much as the digital knowledge base sounds good in theory, I don't think it will ever be as optimal for generation of thought. If all you want to do is summon existing information, digital tools are evidently superior. I personally think a hybrid system where one "thinks" on paper and "archives" digitally (after the thinking is done) might be best, but ultimately, we will be most productive with whatever system we actually enjoy using.