I started to feel the same need as my graph started to grow more and more. Hashtags are some way around it, because they don’t show on the main graph, or eventually you can add URI links to a specific note, they don’t leave traces on the main graph.
But those are just workarounds for a feature that would be very useful - having two types of links throughout the notes, easily switchable on & off on the graph. Tags can go only so far, and they often serve a different purpose for me.