Stacking Penalties were introduced due to counter fail-fitted speed boats (people fitting their ship with nine (9) speed Fittings, being extremely fast). Stacking Penalties (as the word says) reduce the effectiveness of Fittings which provide the same stat (bonus). Do note that Skills and Gunpowders are NOT effected by this!
This information is provided by the update that PotBS Wikia is undergoing, by Captain Vuur.