The stats listed for the equipment pieces are just the base stats, and do not reflect any skill bonuses. The elemental damage bonuses, Stun, etc are applied properly for weapons, so I would assume the same holds true for Augment Defense. With the weapon damage total and armour rating already requiring some calculations, including the 'augment' skill bonus is pretty straightforward.
I have not used the same character/equipment to let the same opponent hack away for awhile with and without Augment Defense, to see if the damage values are statistically different. However, lots of people have played the game multiple times, and I've not seen any reports that people don't seem to notice it working (people noticed True Shot didn't help in the disk version, or a couple of the weapon expertise skills in the unpatched original release).
I'd say it is very likely the bonus is used during the combat calculations, it just isn't shown in the equipment stats.
If you want to test this, though, use
iZakaroN's SaveEditor (or from
Kiya's site, with description) to get a new character to a high level, with very high hit points, and let a strong character beat on you for awhile, while you write down the damage done (20 or 30 values should be enough). After that, learn level 5 of Augment Defense and repeat. You may want to use
DAD's item editor to get half decent armour to start with, so a 50% bonus would be significant.
