If you could develop semantic relationships with cards, you could certainly do it in software. I suspect that actual semantic relationships were discovered simply by constantly reviewing the notes that have been created. And, of course, after their discovery, a system of notating relationships. So the actual discovery was done by the "wetware" in his head, not the "paperware" of the cards. Cutting edge software that emulates neural activity is beginning to do this.
For us, TW has at least 3 major ways of linking information (Tags, fields, links) which should make review and discovery easier than ever. However, there's always that temptation, once data has been captured, to not go back and review.
-- Mark