Stellaris is completely and totally soft sci-fi. Absolutely any explanation of disruptors is basically garbage from top to bottom, much more so than any other weapon because the way they operate is dependent on also knowing how OTHER totally soft sci-fi technologies work - that being the shields they pass straight through.
With soft sci-fi the trick to maintain suspension of disbelief is not trying to explain how the things work. It's to have specific rules of what they do and then sticking to those rules so the audience can just accept that a certain thing does a certain thing. We don't, after all, tend to have any idea whatsoever about any part of the process that happens to allow me to flick a switch and get a bright light, we just know the names of some of the stuff and what it will do.
Disruptors don't just ignore shields....they ignore armour. That's the part which makes them so impossible to try and explain, and makes them space magic powered by authorial fiat. It makes no sense how a disruptor can pass through armour without damaging it while still damaging the internal hull. It is, however, a consistent rule so whatever I don't care. They're like 40k bolter rounds. Through illogical space magic the 'mass reactive' warhead of a bolter shell somehow knows when it has penetrated into a target, despite targets having wildly varying outer layers ranging from all types of armour and clothing to bare skin which can also be of wildly varying density and toughness, and explode inside. It makes absolutely no sense, but it's just what they do, they do it consistently (even to the point of extreme close range potentially not allowing the warhead enough time to arm and pass straight through the target in different books by different authors), so there's no problem.