If you index everything together you get something that it is merely a pile of searchable things. You do not experience the "conversation" with the slip-box as Niklas Luhmann described it. Software like http://zettelkasten.danielluedecke.de/ that implements the "digital version" of the system suffers from what I like to describe as the "Hudsucker Proxy" problem: A young idealist visionary comes out and holds a big plastic loop and mutters "You know... for kids!" and nobody has a clue what that is supposed to mean. It isn't until someone shows how to use the "big plastic loop" before anyone understands what's happening. And that's really hard to do with something as abstract as a Zettlekasten despite it just "being little notes gathered together with lots of numbers and letters pointing at the other notes" or an "unordered database".