Why can a PC cleric pick up a weapon and deal an extra 1d8 fire damage at will? Why can a PC fighter score crits on both a 19 and a 20? That's a learned skill, inherent ability, or other such trait, right?
Why does the PC cleric have proficiency in Wisdom and Charisma saves? Learned skill or other similar ability from their cleric training, correct? As detailed in the cleric class description.
So the 2014 mage NPC has proficiency in Intelligence and Wisdom saves, but there's no explanation as to why. Like you say, they just have that, and it's obvious from the stat block. Why is the NPC guard proficient with spears? Well, they just have that ability. A PC wizard doesn't have proficiency in greatswords because the wizard class doesn't grant that, as described in the class description.
So we have many traits that are omitted from the 2014 NPC stat blocks, and no one's complaining really. Why does the mage have a d8 HD and proficiency in Arcana and History? Well, because they just do! Because those are listed on the stat block, it means they get them. Simple as that. Why is this NPC proficient with the greataxe but this other one is not? Why does this NPC have no saving throw proficiencies at all? Well, they just don't. The explanation is right there, they don't, ergo they don't have such an ability.
But suddenly there's a problem when the 2025 update comes along. To me, it just seems that the issue is change. It's done a little different, so that feels wrong. All the omitted traits in the 2014 NPC stat blocks are fine, but the change in the 2025 version is wrong -- even though the 2025 versions follow the exact same logic as the 2014 versions: you don't have to include every single trait that applies an always-on adjustment to the creature's abilities.
The PC cleric can deal extra damage with their weapon and the PC fighter can score more critical hits because they have a learned skill or an inherent ability. The exact same reasoning applies to the NPC stat blocks. The NPC can deal extra dice of damage with a weapon because they clearly have a learned skill or an inherent ability -- but we don't have to spell it out because it's evident just from the fact that it's featured on the stat block, just like their HD, saving throws, ability score totals, skills, vision traits, etc. We don't include a trait "Drow Darkvision: Drow have superior darkvision up to 120 ft." for drow NPCs, because simply having "Darkvision 120 ft." in the vision section is plenty enough. The reason why the drow NPC has 120 ft. darkvision is due to their inherent ability or learned skill, just like this other NPC's higher damage is due to learned skill or inherent ability.
The aarakocra NPC can wield a weapon with extra damage and magic because it can, the same way it has its particular HD or saving throws or other magical abilities: learned skill or inherent ability.
My issue with these complaints is that they are applied incredibly inconsistently. Why is this NPC's inherent ability or learned skill okay to simply state through its stats without a specific trait that spells it out, but this other NPC's inherent ability or learned skill must include a trait that simply says that the creature has that trait?