From Secrets of SharePoint – Tip of the Day
Previous versions of SharePoint had limitations to folders support for the KPI Lists. Whenever you tried to set Folder as a source of your KPI, SharePoint gave you an error that the folder can’t be selected. To avoid such situation you had to maintain KPI values in different list or use Views. The issue with Views is that they don’t allow you to assign the permissions per View, so you can’t have groups of data and assign different permission for KPI values based on views. The only solution for SharePoint 2007 was usage of separate Lists. SharePoint 2010 fixed this issue, and now you can organize your values per folders in one List for KPI’s.