The Klingons can research a special ability called Combat Tractor Beam, which allows all their Heavy Weapon Platforms to hold an enemy vessel inplace, without disabling its shieldings. There is no normal tractor beam at all.
Such "Counter Weapons" do already exist, like thePoint Defence ability of the akira or the Remoores ECM aura.
Every unit has shield HPs and hull HPs (HPs = hitpoints). If the shields go down, the hull is the one to sustain the damage. If the hull is broken (0 hull HPs) the sips is destroyed.
We'ra actually discussing about adding different types of armor to the game, but this is yet undecided.

I think he means ablative armour, like on SFC:3 and now on BC.....but i don't think thats possible in A2......