Honestly? It depends on if the villain pre-existed.
If I've established that the evil blackguard uses a +2 Orc Double Axe (and it just so happens a PC is a half-orc), and then that character dies and is replaced by an elf, the blackguard doesn't get a +2 longbow instead.
But an evil bandit lord with a magic bow might appear...
One of my inspirations is J. Michael Strazcynski, even if I can't spell his last name.

He talked a lot about the concept of trap doors, of ways to change the overarching plot going forward without changing what's already happened or introducing gross inconsistencies. He was dealing with actors and contracts and the variability of conducting an ongoing series; I (and every DM) is dealing with random rolls and the chaos known as "the PCs". You've got to be flexible.
I just think there's a difference between the DM altering the world, and the rules saying the world has no form.
God can work miracles, but when he's not paying attention, the world has natural laws which keep things going as they should.
Ultimately, a real problem for me is the way the current 4e rules seem to box me in. The 3e MM wasn't just a book of Things For PCs To Kill -- it was a book of starting points. The rules allowed me to staple any class, template, or level to damn near anything. Anything with an Int score could be an NPC, and have any skills, feats, classes, or powers I needed it to have. Kobold manservant? Hobgoblin bodyguard to an elf prince? Orc wizard? Ogre shaman? Half-silver-dragon artist/dilettante? Half-troll/half-green-dragon bandit chieftain? Half-fiend medusa rogue pretending to be a mind flayer? I've statted 'em all up.
4e, it's "Lurker, brute, controller". It exists to appear, beat up the PCs for five rounds, and vanish. It's boring and constraining and limits my creativity to deciding what combat role something should have -- as opposed to building a creature FIRST and then seeing where its abilities and powers naturally place it, if it even is SUPPOSED to be in combat. I've had a lot of fun with NPCs who wouldn't last five seconds in a straight-up fight, but 4e doesn't have any place for them as mechanically distinct creatures. Every ability in the game is centered around combat; anything outside of the battlemat is pure handwaving. Looking at the sample characters, and now we've seen a lot of them, I don't see a single feat or power which is intended to improve performance in "skill challenges" -- the system seems to be an afterthought. You can't, from what we've seen, build a scholar or a diplomat who is actually focused on those abilities; you are Trained in a skill, and that's it.