one more thorugh example to beat this point to death
ship with 5 shield, 9 armor, 1 point defense
effective armor= 9+int(sqrt(5))+int(sqrt(1))=9+2+1=12 armor
effective shield= 5+int(sqrt(9))+int(sqrt(1))=5+3+1=9 shield
effective pd= 1+int(sqrt(5))+int(sqrt(9))=1+2+3=6 point defense
so 5/9/1 is functionally 9/12/6
it pays to hit those squares

at least the first 1 or 2 of them anyhow. later in the game tho the usefulness of this diminishes.
1/1/1->3/3/3. nice. not terribly space or money efficient using those early techs tho. cost you about 100bc and most of your space to do that on a medium hull i think, but you didn't have to do alot of research so...
40/40/36->52/52/48. that take 4 of each of the top defense techs tho. lot of space not used for weapons or engines there. unless your riding military bonuses to get there it just is not practical at that point. better to specialize later in the game. by later i mean sooner
and yep, tho the devs have said that it is 0-n on both weapons and armor i have never seen a 0 dmg where armor was not involved, and if i don't think i failed to notice an attack not reported due to a 0 attk(possibly i did tho). so i work on the 1-n attack and 0-n defense theory.