Hello Antoni,
I'm not quite clear whether you're asking whether that can currently be done in Hauptwerk, but assuming that is indeed the question:
Swell boxes actually affect the sound in ways beyond just its amplitude (volume); for example, they also affect the timbre of the sound significantly (typically reducing the upper frequency content to some extent when closed).
It's possible for a sample set creator (or Custom Organ Design Module organ definition creator) to enclose any given virtual rank in a virtual swell box (or even two swell boxes), and a sample set can have any number of virtual swell boxes, but it isn't possible for the user to change which ranks are enclosed, or for the user to control the amplitude of individual ranks in real-time (except via the voicing sliders, but they can't be controlled from MIDI expression pedals).