Do "super", "hyper", "ultra", "meta" actually mean anything different beyond just being "cool prefixes" that cycle in and out of favor either organically or suddenly when a major entrepreneur just comes along and names their entire ecosystem after one of them?

I know this wasn't the real point of this, but yes, of course they do.

They're mostly adverbial / preposition elements.

Super: above (Latin)
Ultra: beyond (Latin)
Hyper: way beyond (Greek)
Extra: outside (Latin)
Meta: among, between (Greek) -- this one even early on has additional metaphorical usages.