What is 1 hitpoint? Is it a 1x1 meter armor plating? Is it a bolt? Is it a 10x10 cm of iron?
You might as well round it down to 6 million, and simply "imagine" that each individual 1 hitpoint is now slightly buffed in "reality". Maby now it equals to 2x2 meter armor plating.
Why does it have to be a 1cm2 of armor plating? Why not .34543cm2 of armor plating?
Also, I take each hit point to be exactly one nanite worth of armor, capable of defending against any attack from any direction. The final hp is representative of the 'core' of the ship, sans all armor, as if it was the very weakest part, with no shielding whatsoever, and any sneeze in the wrong direction would break it.
Engineer repair beams build nanites and send them on their merry way to buff the armor of any ships nearby, but each ship can only maintain so many nanites due to cpu issues. Space planes have virtuallly none because they are busy being fast and cloaky and shooty. Factories use these additional nanites, and they are added to the factories own control system/nanite production to create more ships.
I add to this that each attack is actually particles of antimatter as well - Each particle is enough to react with a single nanite, stripping 1 hp from the target. Shields relate to the cohesion of antimatter, with higher shields meaning they are more likely to destabilize the attack, stopping it harmlessly through some projected field (lets go with a magnetic one, although gravimetric would work as well)