Assigning departments to a specific layout allows you to limit information (such as posts) to the layout when a person has not yet logged in.
An example of this is if you have a Kids department, a Music department, a Kids layout and a Music layout. If you have allowed guests to view posts without logging in (this can be done in your settings), those guests are going to see posts that are related to Kids and Music if they are viewing the Kids layout. This might be confusing since they are probably only interested in posts related to Kids.
However, if you assign the Kids department to the Kids layout, only posts relating to Kids will be displayed.
Once the guest logs in, it will then show posts relating to the departments the volunteer is assigned to as per usual.
Not selecting a department for a layout means no information will be limited when guests view a layout.