My understanding is that the velocity value of the struck key only affects the first part of the pipe sound. In some organ sample sets, the rapidity of the valve opening is controlled by the velocity value of the struck note. Once the pipe has passed to the full volume part of the sample the velocity usually will have no effect on the sound. As the valve will close by its own timing the will be no change in the end of the pipe sample. There are exceptions however;
Hauptwerk Manual pag. 286: Some virtual instruments are able to respond to key velocity. Hauptwerk provides a tracker action model which enables key velocity to be used to adjust the initial speech of pipes, or to select pipe samples dynamically amongst several different-velocity samples
This is unlike a real mechanical pipe organ where the opening of the valve is controlled by the position of the key and not the velocity and the closing of the valve can also be affected by how quickly the player removes pressure from the key. (i.e. legato playing).
The main use for velocity sensitive keyboards in electronic organs is the playing of MIDI pianos or other instruments which require a velocity value of the note to provide expression. The best example that comes to mind is Pierre Fracalanza and his Garritan Steinway/Paramount 450 organ setup.