The Vorpal Blade and Sword of Sharpness date back to the Grayhawk supplement of OD&D – the White Box/Brown Book days. Before that, there wasn’t even varied damage by weapon type. Those swords are indeed clearly inconsistent with the idea that d20-triggered damage bonuses are some kind of off-the-map crazy stuff.
At that time, Gygax was still pretty openly encouraging house rules – the idea that the D&D rules were just guidelines. I think it was not long after that – still a couple years before AD&D – that he became very defensive about copyright infringement and unauthorized game supplements. I don’t know whether that was driven by financial imperatives, fear that the game was becoming “trivialized” by loose GM-ing, or simply offense to his ego, but he soon fell back to the stance that pretty strict adherence to the official rules was necessary for a game to be “real” D&D, and that anything else was an “inferior product”.
Yes, when the guys at Chaosium pointed out the absurdity of increasing encumbrance making one harder to hit, Gygax et al retconned it to say “we meant damage when we said hit”. Despite this, later editions still all used the word “hit”.
This was a fairly weak and absurd rationalization, anyway, to anyone who has done any sort of armored combat. If you are more encumbered, your opponents will land more and heavier blows on you, which will inevitably do damage to your armor, which will restrict your movement and agility even more, so that the crowd of peasants with hammers ends up with a battered and immobilized can full of Knight in the mud, until one of them steals the misericorde and administers the coupe de grace through the eyeslot or under the paulder. D & D armor, of course, is generally undamaged after any number of combats, but can be destroyed by any number of other, lesser mishaps.
In SCA full-contact rattan fighting, Visivold used to fight in a purple gown made out of thin mattress padding. He was such a superb swordsman that nobody could land a blow on him, so it didn’t matter much that this was against the rules and extremely dangerous. Sigfried von Halstern once dismembered my (borrowed) leg armor - apparently just for fun - in the middle of a huge field battle, carefully blasting off a row of copper-riveted plates one at a time, without actually touching my thigh at all. D & D’s combat system (or any system with so few states in the table) can’t accommodate any of the artistry and subtlety of real combat without GMs just abandoning the rules and cutting from whole cloth, and simply can’t simulate the kind of things expert fighters do.
As @Tnyam points out, it was odd that Gygax was so adamant about all this stuff, when he could have just used the (perfectly valid) answer that game designers have used since Backgammon was the new shiny - “it’s fun to play this way, which is the whole point of a game, so we don’t want to change it”.
I cast a fairly jaundiced eye whenever someone starts pontificating about “realism” in simulated combat, whether tabletop or of the quasi-LARPing variety. LARPers, of course, are usually just acting out D&D-type games, but although some members of SCA try for more realism and verisimilitude, they in turn get looked down by more “authentic” reenactors. In the book Confederates in the Attic by Tony Horwitz (which I heartily recommend to anyone who is interested in how the American Civil War endures in culture and society today), the hardcore Civil War reenactors refer to the less authentic weekend warriors as “farbs”; the etymology of the term is uncertain, but my headcanon backronym is that it stands for Fucking Amateur Reenactment Bastard. The hardcore types not only insist on clothing and gear as close to the original as possible, not only in material but in construction, but also try to duplicate the experience of the soldiers as closely as possible (eating rancid bacon, huddling together for warmth, etc.).
But, really, even that’s just kidding themselves, because those guys can always just go back to wherever they stashed their keys and wallet and return to a lifestyle that’s as far beyond anything that Johnny Reb and Billy Yank ever experienced as the world of Star Trek would be to ours. When you find out that even some of the so-called experts can be wrong about the salient details, “authenticity” and being “hardcore” seem a lot less important than having fun (which, at least in the SCA, according to friends who have participated, is the real point). I used to game with a GM that gradually drove his players away by insisting that we know our encumbrance at any given moment, or that we find a money-changer every time we went from one tiny kingdom to another, or other persnickety details. In a game that involves crazy spells, gelatinous cubes and beholders, it’s not all that important that my halfling rogue can carry more than her body weight and still be stealthy, as long as we’re having fun.
This is part of why I moved to Story Games like Apocalypse World where the GM simply doesn’t roll dice. The game is about the story, the characters, and fun, not about dice mechanics and randomness, especially on the part of the world. Why should the monsters need to roll?