Hello Richard,
The current version of Hauptwerk (v7) doesn't have any additional de-bouncing capability beyond what's in v4.2.1, which is basic, but sufficient for most cases. In v4+, if a piston's 'Prevent rapid re-engaging (de-bounce)' option is ticked Hauptwerk simply ignores any MIDI message received for it if it's within a few hundred milliseconds of the last. Debouncing within the MIDI encoder hardware/firmware would always be preferable.
Here's another thread relating to debouncing:
viewtopic.php?f=4&t=19444&p=145920#p145920