As a static graph of an entire database it can have readability issues, but certainly what would help is having the graph update based on where the user is focusing their attention.
For example, if the graph focuses on the currently active document and highlights only the connections of up to X degrees of separation (ideally user adjustable) then that would help a lot to contextualise the current document. If one could then click on one of the related nodes to “walk” through the graph and have the graph then dynamically update to centre on that node then this would allow one to follow a chain of related thought.
This could therefore be an additional way of navigating through one’s notes rather than browsing through lists of items in a given Group or Tag. Furthermore, it complements the AI functionality in helping expose related notes to a user.
One other thing to note is that even in a database of thousands of documents, not all documents would have a x-devonthink-item:// link in them - only the notes where a user has explicitly made the connection.