Why does Jawa Engineer need so many Stun Cuffs?

Damage is percent health based, you are not missing anything, you are throwing many stun cuffs at him in order to go to the next gear level.

This is just a repeat of "why do I put equipment with attack on Grievous" or "why do I equip B1 with things that give health" or "why does Hoda equip things that give potency or attack or crit chance". You do it because CG has decided that you'll have to grind, so get grinding.