The limb cannot be targeted separately by sunder
My interpretation of the phrase
"You can attempt to sunder an item held or worn by your opponent" Sunder
is that the grafted limb could not be the target of a sunder check. It comes down to the definition of "held" and "wear" but I would not say you hold or wear something that is permanently attached to your body. The wording for the clockwork arm specifies
"to function as a replacement arm" Clockwork Arm
which I would interpret as acting the same as a normal arm in all ways except those specified in the item description. Since you can't sunder a normal arm you can't sunder a clockwork arm.
Necrografts also specify that they "replace" the missing body part but are less clear on the "function" language.
If the limb can be targeted
If you disagree with my interpretation of those phrases then the limb can be targeted just like any other wonderous item. Looking at Damaging Wonderous Items we see this.
"Magic items, unless otherwise noted, take damage as non-magical items of the same sort. A damaged magic item continues to function, but if it is destroyed, all its magical power is lost. Magic items that take damage in excess of half their total hit points, but not more than their total hit points, gain the Broken condition, and might not function properly" Damaging Magic Items
Since there are no exceptions stated in the item descriptions I would go to the Damaging Objects page and figure out AC, Hardness, and Hitpoints from the tables.
You might say a leg is small while a forearm is tiny on the AC table.
For materials, a clockwork arm might be steel or mithril; however, necrograft again gives us a problem here since there is no entry for flesh. You might compare it to leather, but just the fact that there is no entry on the table leads me back to the belief that they are not meant to be targeted separately.
If the limb gained the "broken" condition, it would need to be repaired in the same way as any other magic item.
Dispelling the limbs
This has been answered here: How are clockwork prosthetics and necrografts affected by effects that cause magic items to stop working?