We have visualizer installed in the app servers.
When we open any CI in the visualizer it displays the active as well as inactive CIs. We have removed the relationships from the inactive CIs, however we can see it in visualizer.
As I understand from my chat session, the inactive CIs are displayed with a RED box surrounded around them.
We checked in the r12.1 version and found that Inactive CI's were not visible in Visualizer, hence would request you to take it up as enhancement and confirm.