I have a synology diskstation with over a terabyte of music. Using the control app I can access all of it, but it can take quite a while to scroll through screen after screen to get to specific items. There must be a way to manage content better and easier than this.
The Pioneer ControlApp is just a remote control plus on board screen substitute for the N-50. So you can't do anything on the ControlApp that the N-50 (via its screen & remote or buttons on the box) itself can't do.
The N-50 relies completely on how the UPnP/DLNA media server takes care of the music library and thus displays exactly what is given to it. The choice of UPnP media server therefore determines the navigational experience and has nothing to do with the N-50 itself. With such a large music collection, you ought to be using a decent UPnP media server is designed with music in mind, such as the excellent free MinimServer, see: http://minimserver.com/features.html
Be prepared to be a bit hands on making sure your music files contain correct and adequate music category tag data. This will help the media server build the music library into a better managed & navigable structure.
You can also use a decent UPnP/DLNA controller, such as the BubbleUPnP app for Android, for more advanced navigational features, eg, UPnP searches and build & save playlists of your music.