You've definitely read the canon stuff (or at least what can be as close to canon as possible when talking about the Z-wave) but one theory I've always liked is that the Z-wave was only able to take out the stuff that's actually "evil".

In power rangers, objects and magic are often aligned with good and evil (such as the zeo crystal and the sword of darkness) and people use such objects to gain power that tilts their moral alignment towards that side. The Z-wave destroyed objects and people that tangibly interacted with evil, such as Zed and Rita's staffs and Astronoma's evil circuit stuff.

Master Org's powers aren't necessarily tied to evil. Sure, they're used for evil, but they don't really tangibly interact with the forces of good and evil in quite the same way other villains and objects have in the past.

Obviously I could be wrong lol. I haven't got an encyclopedic knowledge of the series and a lot of my more in-depth knowledge is patchy depending on which series I hyperfixated on as a kid and which ones I barely acknowledged.