A number of applications (Plasma Media Center and Amarok) would like the ability to control which folders are indexed. We should provide an API for them. Relevant Code: nepomuk-core/services/fileindexer/fileindexerconfig.* The class should provide at minimum methods to change the list of indexed files. It doesn't need to provide all the other fancy features present in the FileIndexerConfig class.
Thank you for taking the time to file a bug report. The Nepomuk project is no longer included in the KDE Software Compilation. With Plasma 5, we have replaced most of the underlying technology with Baloo and other components. Hopefully this will have addressed your concern. We encourage you to try to Plasma 5 (+Baloo) and let us know if your problem persists.