Well there are times when it is illogical for the armor to be missing.
In ENT, when all weapons are weaker we should have seen more armor. If an Augment can withstand being shot at, then armor can do the same. Also where has all the headgear gone?
I agree with the idea, that if a weapon does not disintegrate a person, then armor should offer at least some kind of protection. And the Federation ought to care about the health of its people.
I also question, why doesn't the security personal use some kind of riot gear?