Your post came at a perfect time for me. I had actually assumed embeds did show up in graph view, and I was just starting a new document and workflow under that assumption.
That would have been a sad realization later. Thanks for the heads up. Maybe I will just add normal links in headers above the embeds.
Edit: Just checked and realized that embeds in fact do show up in graph. I see now that you were talking about situations where you hide your atomic notes.
It may also be interesting to have depth options to allow the graph to have settings to show links from a note with an embed to the notes embedded within that note and so on.
Good idea.