This sounds easy adding more hitboxes isn't actually the answer.What I propose instead is: let's divide the arm hurtbox into 3 parts:
arm, elbow, forearm.
For example you say each unit has 6 hit boxes currently. That means in a 1000 man battle the CPU has to calculate 6000 different hit boxes. Now lets say we go with something like your suggesting. You would probably have 2 hitboxes for the head, 3 for each arm and leg and maybe 6 hitboxes for the torso front and back. Now all of a sudden in a 1000 man battle you have the CPU calculating hits for 20 hitboxes per unit or 20,000 hitboxes for the entire 1000 units. That is more than 3x the amount of hitboxes the CPU has to currently keep track of and the game is already one of the most CPU intensive games out on the market right now. The question then becomes, what do you want to give up in order to add 3x the hit boxes?
I guess we could dial back the battle size to a max of 300 units for a top gaming rig with a top end CPU leaving lower end gaming rigs maybe with 100 max units on the battlefield at a time, however, I strongly doubt many people would think giving up 2/3rds of their current max army size as being worth having a more accurate armor damage model.
This is why you have to look for simple solutions to try to correct the problem. For example, adding to armor values, lowering weapon damage or changing some of the multipliers on the other hand cost no additional CPU processing power and while not the most perfect solution might actually provide results that feel much better if still imperfect.