because that's the way the game mechanic works.
some hits just pierce through the armour and hit the modules, without hurting the structual integrity (hull) much.
but i have to admit: it doesn't make much sense (unless the hits hit a hole that was previously punched)
It makes sense. A lot of targets are outside ie engines sensors weapons shield unit. Others like powerplant drive have a hp, lets say 200hp for powerplant. 30 of those hp are hull (you only need to make a hole once) the other 170 the powerplant.
Perfect sense.