
Hello James,
From your description, I would guess that you're referring to residual noise reduction artefacts in the samples themselves, which are impossible to eliminate entirely when making a sample set of an organ, especially due to the presence of the (real) blower and the need to use noise reduction software to try to remove as much of it as possible as unobtrusively as possible. If so, then Hauptwerk v5/v6 couldn't lessen that (since it would be in the samples).
If the high-definition pitch-shifting and/or 96 kHz options are enabled v6 will significantly reduce overall *playback* distortions, usually giving noticeably improved overall clarity.