In my opinion the daily notes should show up at either the top/left/right/bottom as a timeline, ordered sequentially. They should still be linked to everything else but not be considered in the force direction of the graph.
This would allow me to hover over notes across time, and see what they were connected to effectively telling me what I was thinking about most over that period.
Daily notes are clearly a different category of note, which is why we get requests to remove or filter that view (Remove log days in graph overviews) but I think showing it in the graph is still helpful.