Old, pre-Cata Hyjal was dummied out, and everything in there was not supposed to be viewable at all. At this point we've seen the version of Hyjal we were supposed to see, which is the version we saw in Cata, which didn't have a giant skeleton. That would be the canon version of the site.
Which means that Archimonde's skeleton didn't go anywhere. Archimonde exploded and didn't leave a skeleton behind.
I think it got scrapped because it contradicted WC3's version. Archimonde explode into nothingness in WC3.
I'm pretty sure that's the official explanation. That skeleton was never supposed to be there. The area you could see before Cataclysm was nothing more than a placeholder. Archimonde was pretty much vaporized when all the wisps exploded on him, and he left nothing behind. Maybe someone at Blizz got bored and decided to toss that in there for shits and giggles, thinking nobody would see it anyway.
This is Archimonde's death cinematic from WC3, and you can see that there's pretty much nothing left after:
A bit offtopic, but I remember sneaking into Hyjal back in vanilla.(used to be able to jump up some rocks in Winterspring (by the locked gate in the demon area) and the only way out was to hearth or jump off the platform where the fire druid chick was in Cata.
I think the true question is that why the hell it was even put there? He literally got flashed to nothingness in the WC3 cinematic, leaving no skeleton whatsoever behind.
I might be wrong but iirc Hyjal was supposed to be a vanilla zone but it didn't get finished in time.
Maybe a designer developed the zone (Hyjal) but he wasn't exactly a lore nut and didn't know the specifics (Archimonde turning to nothing) and so he made the skeleton, but it would have been removed before making it into the game as a zone.