The Kunena team has announce the arrival of Kunena 6.3.0 [K 6.3.0] in stable which is now available for download as a native Joomla extension for J! 4.4.x/5.0.x/5.1.x. This version addresses most of the issues that were discovered in K 6.2 and issues discovered during the last development stages of K 6.3
You can do it only manually. Go in the backend to "Kunena -> Tools -> Prune Categories". Choose a time period -> Select the Categories and to prune only Shadow topics (see image).