@benoit.pointet is really really close to having this working as a script - see Graph view : a network visualization script for DT - #18 by benoit.pointet and also see GitHub - benoitpointet/devonthink-graph-view
This was clearly an immense effort on his part - he is working on making it work with WIkiLinks in DT3 and then I think it will basically have achieved what you are suggesting.