That's not entirely true. Armour does decrease effectivity of weapons doing lower damage per bullet, true. But it's not linear regression. Armour works more effectively against damage which is higher then armour DR value itself. When damage is lower, proportion of damage which is negated does not equal to ratio between damage and armour. That to certain degree negates disadvantage automatic weapons have and they can still outperform their semi auto counterparts in DPS at the end. This is especially true against very heavily armored targets sine it does not really matter if weapon is doing 10 or 20 damage when damage resistance of armor is 200. Difference between 10/200 or 20/200 is negligible.
Weapons with single shot damage high enough to make difference against heavily armoured targets (means 100-200 or more) have terrible fire rate and you don't want to use them in close encounters. If you are under attack by pack of ferals and you have only gauss rifle, then you are pretty much dead. There is not one size fits all in Fallout 4 and high fire rate have it's uses.
And then, lot of automatic weapons have armour piercing mod. Unfortunately I have no idea how exactly does it work. Do somebody here have any info?
I am finding again and again, that at close ranges, the most dangerous enemies are usually those with automatic weapons. Although it always is situational. Sometimes shotgun to the face is more dangerous
I have to say I quit like how armour works in F4, so far it's best armour system in any Fallout. previous Fallouts were all quit a mess since they worked with absolute not relative numbers. The obvious indicator that it's well designed is fact that there are no hard caps like in F3/NV. Whoever came up with this new system deserves praise. So kudos to developers!