I feel like it's pretty clear that Hythlodaeus wasn't sundered, and what happened with the souls within Zodiark was essentially that the collection was split up rather than the people within it. Picture it like dividing a crowd; you're going to end up with smaller collections of people, but you're not going to end up with fractions of those people (unless you're extremely bad at it).

It does seem a little weird that Zodiark seemed to be sundered differently like that, but Zodiark was already different to everything else that was sundered, in terms of scale, makeup, and intention. Zodiark was already going to require a fundamentally different approach than everything else, so it makes sense that he has a different end result.

...or maybe it is the same process, and that's just what it looks like when the amount of souls inside a thing being sundered is greater than 'one'. Again, Zodiark is different to everything else that got hit, so we can't exactly prove otherwise.