The Nepomuk kded service should not exist. It exists in order to tell KDirNotify when files have been added and removed from a search folder. Most applications create a kded module cause they do not have a service which is continuously running, and therefore need kded. Our query service is always running. The QueryService can be responsible for informing KDirNotify about files that have been removed and added. Relevant Code: nepomuk-core/services/queryservice and kde-runtime/nepomuk/kioslaves/search/kdedmodule/*
The reason for it being a separate module was to separate the KIO listing from the query service. Without that separation the query service has a hard dep on KIO. While this is probably not such a big deal at the moment it could be down the line when using Nepomuk in less KDEish systems.
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.