The FileIndexing options should be disabled if the File Indexer is not enabled. Relevant Code: kde-runtime/nepomuk/kcm/*
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.