Well arn't they kind of allready in? The special weapons of some ships target a range of stuff from (sorry I cant remember the names of the abilities!) that one that completely cripples a ships movement, shields and guns, to the one that I THINK that robot frigate has of hindering movement?
I know its not really the same as targetable subsystems but its not bad considering the scale of the game. Also I'm not sure how useful it would be in anything other than one on one or small scale engagements because when the fighting gets heavier ships dont last all that long away, so the ability to take out a specific system isnt that important when the things just gonna explode in a few seconds anyway.
However, having said that nexus: the jupiter incident, I thought, handled subsystems really well but then again it was a lot harder to destroy ships in that game.
Anyway my 2 cents