In RMU, you can make a called shot at -25, but the attack is resolved against the selected target location (head, arm, torso, etc). If the armor on that area differs, you use the armor for the location. Generally it's only worthwhile if the location is less well armored than the rest of the body or you specifically need to damage that location (e.g. target only harmed by headshots). Then you roll a critical but reduce the result to the next lower critical affecting the specified area.
For a ship's subsystem... first question is, can it be targeted? E.g. the thrusters are exposed so yes. Life support might be entirely internal, so no, unless perhaps they make some kind of engineering roll to see if they know exactly where it is. If you decide the answer is yes, apply a suitable penalty. If the subsystem is particularly exposed, it might be treated as having less armor. I'm not familiar enough with Darkspace/Spacemaster to know whether those things are applicable or whether criticals specify subsystems....