I guess i'm also suffering from that. I have an "invoice" library that is linked to several other libraries, and whenever I click one item of the library "Company" that Id like to associate with that invoice, it also shows me a lot of diverse libraries related to invoices but that have no relatiom with that specific company.

Any relationship can manually be hidden in a library, but I really only want to hide relationships that have no entries.

I wish I could attach a screenshot right now.