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?
They did in TFF. Shields and assault phasers and all that.
OTOH, it's been overlooked that Klingons wear full body armor everywhere, in every case, all the time. Not all of the time, but sometimes we have seen Klingons appear to at least partially shrug off direct hits from phaser blasts or take a hit without being all the way stunned or killed and it takes a second or a third shot to finish the job. We normally sort of attribute this to Klingons being natural badasses, or adrenaline or whatever. It's probably just the armor; although Klingon armor is mostly ceremonial, it probably DOES provide some measure of protection from energy weapons (the soft/squishy armor in TUC was probably a modernized version that was slightly more effective against phasers but not as popular with the warrior caste).