No one in their right mind is going to target a limpet controller so any damage to those will be collateral. And if a fight reaches that point you'll usually have bigger worries than whether your limpets are fine. Put another way, the only times when a limpet controller dies on me is when my ship blows up.
If I bother with engineering a limpet controller at all it's lightweight. Shielded/Reinforced is a good choice for a point defense and maybe chaff/ECM/life support, on any other module though they don't really offer any (noticeable) benefit.