You're going to need to modify retail tables to assign the said subsystem an armor type to begin with (well, to the same extent as just changing the HP) - a -shp.tbm, unless you seriously plan on setting it for every single mission it appears in.
As Fury noted, if you ALWAYS want the effect on, there's no reason to mess with setting up an Armor.tbl, especially if you don't need to modify subsystem resistance on the fly.
I'm not against using armor.tbl (hell, I'm using it in my own mods because I want to have different resistances to different weapons an I love it), but to set up the whole thing just to toughen up a subsystem or two is severe overkill if you don't plan on using anything else.