They DO have separate cooldown. releases have cd of 1 while barrier 3.

I dunno how WKI works, but I know that dance SHOULD reset both (tested with haku, turn 1 haku barrier, turn 2 dance THEN haku release, haku is able to cast barrier again). But it doesn't work for sasuke (and I imagine Gaara), as the same sequence result in cd 3 sasuke barrier.

So either one of the following two could be happening:
WKI only resets the release and not the barrier (since it specifies the kill mystery is the one that is reset, as opposed to dance which is 'all")
WKI did reset the barrier, but then the release sets the barrier to 3....

To tell which it is, you'd need a different barrier, to see if the release of the barrier killing things would reset the barrier itself. I'm not entirely sure how WKI works on the reset part, does it only do it for swords or does it work for any ninja? If it's just swords, then I'm afraid you can't find out now, as sasuke is the only one. But if it's any ninja, you could try Anko (sasuke/gaara are bugged, haku can't kill, jirobo/yamato don't have releases.... so... not much choice)

No, I was wondering how WKI works with sasuke BEFORE the last update (which, sadly, cannot be emulated with other ninja as it's the only swords manual barrier I think)

I would guess barrier replacement is still as it is before, working on a similar mechanic as barrier expiration, which is unchanged. It's only when you cast Kirin that everything goes to heck.