Hello Tim,
When routing to a stereo output:
1. If you load a truly mono sample into Hauptwerk then it will pan it into stereo using the virtual pipe position information specified by the sample set producer within the organ definition. There is no loss of quality involved, compared to playing the mono sample in mono.
2. If you load a truly stereo sample (i.e. one with independent signals in its left and right channels) in mono (but route it to a stereo output) then Hauptwerk will pan the mono-loaded sample into stereo using the relative channel RMS levels detected from the original stereo sample. The panning doesn't lose quality in itself, but loading a truly stereo sample in mono inherently loses quality/information.
3. If you load a stereo sample that itself was made from a panned mono sample (i.e. that doesn't have truly independent left and right channels) in mono then Hauptwerk will pan it back into stereo as described in 2. However, since the two original sample channels weren't independent in this case, no quality/information would be lost by loading the stereo sample in mono (or by panning it back into stereo).
I don't know off-hand what Sonus Paradisi do within their samples or organ definitions, but I would imagine that 3 would apply (i.e. that the separate left- and right-samples would actually each be mono samples hard-panned into stereo files, so there would be no loss of quality by loading in mono but letting Hauptwerk pan them back into stereo). You would probably need to contact Sonus Paradisi if you wanted to confirm that for certain.