EMP is a type of secondary damage dealt by some weapons, and the primary focus of Ion weapons. EMP deals negligible damage to shields, armor and hull, but is very effective at temporarily disabling an enemy's weapons and engines. Some weapons, such as the Ion Beam, note in their description that their EMP component can pierce shields based on the target's hard flux level, but outside these special effects, EMP damage is effectively negated by shields.
Advanced Info and Calculations
Actual effect is somewhat inexact as the EMP damage is proportional to the distance between point of impact and the weapon or engine, believed to be similar to the damage pattern for armor cells, except it does half-damage to the primary/secondary cells and quarter damage to tertiary cells.
This means that broadly speaking weapons set further into the hull will take less EMP damage as they will likely be further from the point of impact. Some niche cases exist where the point of impact may be in the middle of the ship, such as Ion Cannon armed Claw or Thunder Multirole Fighter Wing firing during overflight.
Weapon durability is 250/500/800 for small/medium/large turrets. Doubled if a hard point instead of a turret. Potentially doubled by Armored Weapon Mounts. Engine durability is based on hull size and size of the engine plume, with bigger engines on bigger ships being more durable.
Exact engine durability is a baseHP of 100/200/400/600/800 for fighter/frigate/destroyer/cruiser/capital and the following formula, where "size" is engine glow width + height, clamped to [0, 100]
maxHp = baseHP * (0.75 + (size/100 * 0.5))