I don't really have too much experience with 3rd Ed, so take this with a grain of salt.
The rules for Manei Domini are in Jihad Hotspots 3072. As far as I am aware, advanced prosthetic limbs don't provide any additional protection, but prosthetics can be damaged separate from the person, and advanced models can take more punishment, additionally, the advanced models can contain tools and equipment including weaponry, I think there's also a strength bonus, but JHS 3072 refers you to a table in the main roleplaying book. At any rate, the limbs themselves are pretty much going to be more offensive enhancement.
Manei Domini soldiers can get implants that help their toughness, though. A pain shunt gives MD troops the Pain Resistance trait, let them ignore stuns and reduces fatigue and wound effects, and dermal myomer armor gives an armor of 3/3/3/3 and pain resistance while TSM grants toughness amongst other bonuses
