EMP can arc through shields depending on the hard flux of the target at listed percentage rate on a given weapon, I think. There's weapon health which I believe is fixed based on the size of the mount (though I don't remember the exact health values), and then there's EMP damage which is set for any weapon as well as listed in-game. EMP damage ignores the armor of the target to damage weapons and engines (which other weapons have to go through before damaging weapons and engines), unlike more conventional fire, which is the reason why it knocks out those systems so easily. The EMP effect occurs around the point of impact, if the bit above didn't make that obvious. There's also EMP arcing when it hits the surface of the target, which I think can arc to other parts of a ship and affect those areas, though that was added (relatively) recently so I couldn't tell you much on that. I think *some* EMP weapons also have the ability to briefly overload a ship when it makes contact with the hull, though I think the only weapon currently capable of doing consistently is the Tachyon Lance, though the Ion Cannon might also have a small chance (but I don't remember all the patchnotes).
All you really need to know to use EMP weapons effectively is that you have to target weapons and engines and, the higher the hard flux of a ship, the better chance EMP will have of arcing through and disabling systems regardless.
That broadly gels with my anecdotal experience. Hard numbers on size of point of impact, how much durability mounts have and arcing all over the ship would be excellent
Not sure about regular EMP damage arcing through shields or overloads (but not certain either)
Ion Beam & Tachyon Lance are a bit odd as they have scripted effects. Their .wpn files include something like;
"beamEffect":"com.fs.starfarer.api.impl.combat.IonBeamEffect",
and peaking inside shows a lot of code regarding target's shield status and piercing chance, inside
\Starsector\starfarer.api.jar -> impl -> combat -> IonBeamEffect.class
I can't see anything relating to overloads scripted, although the Tachyon Lance is quite capable of causing a regular overload via regular damage if the AI snaps it's shield up to block it (upwards of 2K damage bursts will do that). The Ion Torpedoes from the Ship & Weapon Pack mod actively add flux to targets on hit (via script) but I'm not sure anything else does. A whole ship knocked out by EMP does look very similar to an overload, to me