Create the links manually to create explicit associations because it is an opportunity for you to do your own thinking. Your own thinking shall make stronger associations between your notes because these associations are more explicit. The interlinks of API-like titles in your note-writing system powered through wikilinks are explicit associations compared to links generated by tagging that are only inferred. When you look at a list of notes under one tag, it isn’t explicitly clear how these notes are interrelated. Furthermore, the terms you use in your thinking will change. Creating tags before hand will prevent you from changing organically, because they force lock you into a premature structure.