The atlatl was not in prominent use when the Spanish first appeared on the scene - it was reinvented/readopted when its effectiveness was realized. I'd imagine by the time its use had spread again the Spanish had plenty of cannon fodder in the form of native auxiliaries to soak up the damage. And muskets weren't really a factor - the few guns the Spanish had were obsolete and of limited utility. They did make effective use of ship-borne artillery in the siege of Tenochtitlan, though.
dismal: Don't believe everything you read. Like it was pointed out before, numbers are often inflated to make a battle seem more impressive. You didn't state a source for that account, but it sounds like a propaganda piece. Cortez needed to make his expedition sound glorious - he was actually disobeying his superiors by fighting the Aztecs and his life depended on garnering support though smashing victories. If he didn't win decisively, he either made it sound like he did or painted overwhelming odds nobody could win against.
Anyway, all this talk of equipment is relative. The man behind all the armor and weaponry is vastly more important a factor, as is good generalship.
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