Currently, if a ship has armor that has EMP immunity, it is always EMP immune. Likewise radiation, blind, disintegration, etc. This includes ships with internal compartments. But in order to damage these compartments, we first have to destroy the armor above it.
To make things more interesting, and also give a reason to use status-effect weapons, internal compartments should lose most or all of the resistances provided by the armor that once protected them. EMP resistance should be a tiny fraction of the armor's resistance, radiation should have a much faster time-to-death and have 100% chance to contaminate, and disintegration should always work. This means that blasting through the armor and then using status effects to cripple a ship to make the long, boring grind to actually kill it a lot easier is viable.
If this were to be implemented it would be desirable to have some sort of indicator to show that an armor segment has been breached on a target (unless that's what outgassing is supposed to indicate right now? I was never totally clear on what triggered it.)
Venting and fire is indeed an indication of damaged internal stuff. Making things a bit more visible might be cool though.
I need to consider this holistically as part of an overall improvement to internal compartments (which I agree are a little unbalanced now).