A lot of people advocate creating atomic notes from the start. I actually think that is a waste of time and that you should only excise part of a note (making it into a new “atomic” note) when you want to reference it elsewhere, whether that be a link or an embed. Instead a note should look like an interweave between the notes content and embeds. The primary reason Luhmann used atomic notes is it allowed for the insertion of new information anywhere in the notes collection. In a digital system we do not face that issue because we can edit the text on the fly.
Yes the objective of a zettelkasten is knowledge development, which is essentially the remix of ideas or creation of new connections. Traditional note taking tools do not look to promote the development of knowledge but instead stick to just knowledge management (storing & retrieval of information).
Search functionality is not part of the feature set of a zettelkasten, but instead a more fundamental feature of information management (note taking) systems. Linear search is a nightmare so throughout time we create search tools to facilitate quicker search. In the far past this took the form of indexes, summaries, and table of contents. This is why Luhmann used an index, he needed a search tool.
Nowadays we have digital search tools that make it very easy, so we don’t necessarily need to use an index or other traditional search tools. You might ask why then do I have an index? Well I find that an index can still often be faster than using the universal search tool (the magnifying glass icon in top right corner of forum) because the universal search tool pulls up all the occurrences of a concept, when in reality I only want the first occurrence.
For example, my index takes me to the very first note on “Note Size”, whereas using the universal search tool brings up every occurrence of the word Note Size.