I love the empire overview window. It is the only window that I can find which actually lists my ships. Have you tried to find a scout manually, by zooming around with the camera? In a small galaxy it is a chore, in a large galaxy it is IMPOSSIBLE.
Expand the empire overview's utility by adding filter buttons on top that we can click on or off. Filter out all planets/stars, idle planets, military ships, each ship class, etc. That way if I am looking for something I can find it by clicking a few buttons and filtering down to what I need. I can tell this game is going to run into information overload soon. I am in a 150 star galaxy and only have 6 systems colonized, but already I have a constant stream of events scrolling through the log.
Barring the inclusion of some sort of fleet screen, which would likely take a lot more work, a filterable empire overview window would go a long way towards letting me find the ships I need.