That's what a full-text search is for. The "Zettelkasten" had forced limitations, as a better technology was not yet available at that time. Personally, I find the outliner approach much more practical than a huge set of (possibly) cross-referenced cards, since an outliner provides a priori context. In CrossLine (see https://github.com/rochus-keller/CrossLine), I also built in transclusion, which allows you to integrate items into different contexts without creating redundancy; of course, there is also a full-text search.
Tags are better at connecting notes: if you want to make a two side link, it's equivalent to creating an unique tag and tagging both nodes with it. But in general you can add more nodes to a tag.
