Oh, Hydaelyn did Sunder the Source into the Shards, no question about that. What isn't known is if she is still keeping them separate or if the Source/Shards being separated are "how the world works now" and don't depend on her being there to stay separated. Another thing that may or may not depend on her is the cycle of rebirth that all aether goes though. There's a lot of different processes that Hydaelyn may be vital in keeping going since they don't seem to have existed before she did and we have no evidence either way about what could happen to those processes if she dies or stops existing.

In the same vein, Zoidark rewrote the Laws of Reality somehow to keep what happened in the Last Days from ever happening again (probably changed how Creation Magic worked). He also rejuvenated the planet from all the destruction that happened to it in the Last Days. When Hydaelyn Sundered Zoidark, she specifically did not kill him, but sealed him away. My question is... does killing Zoidark undo what he did to reality and the Planet or does it not? 'Cause if Zoidark's "fix" to reality stops working if he's gone... yikes... out of control magic would be... bad...

One of the really big things that makes killing Zoidark and Hydaelyn different then killing other primals is how much what they do might still be effecting reality as we know it. And we have very little information about how much or how little it would effect reality if they were to stop being around. One the one hand, their changes might be permanent and killing them would change nothing. On the other hand, the very laws we know define how much of reality works might become undone and plunge the world into chaos and reduce several world's into nothing but aether while the aether cycle grinds to a halt. But, we don't have anywhere near enough evidence to know what would actually happen. Just enough to know that both Zoidark and Hydaelyn were created specifically to change how reality worked and change it they did. Messing around with the beings who changed reality in ways we are still not totally aware of sounds like a really, really bad idea.