Currently all the nepomukservices have the lowest priority. This is done so that the user is not bothered with indexing and other details. However, that might not be the best behavior. It would be better for each service to specify what priority level it should be set on. The fileindexer can be given a low priority, but maybe the storage service should have high priority. Relevant Code: nepomuk-core/servicestub/priority.*
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.