Obviously, the Makuta stationed in Karda Nui in 2008 were obliterated by the energy storm that initiated upon Mata Nui's awakening. However, it has always perplexed me as to why they didn't simply teleport out of Karda Nui... it certainly isn't a distance issue, as Chirox would regularily Teleport between the island of Visorak and Keetongu's homeland, which were massive, massive distances away from each other.
Perhaps they were unable to escape because of the Karda Nui shields prevented the Makuta from teleporting through them, in the same way they blocked the Nuva's Suvas (Dropping bars here, excuse me) from transporting the Masks into Karda Nui.
Now, of course Artahka was able to teleport the Nuva into KN, which would destroy this proposition until the method of teleportation is considered. Artahka warps space around the subject he is teleporting, wheras the Makuta teleport themselves the standard way: Dissociating at a molecular level and reconstituting at the desired destination. Artahka is able to bypass the shiels in the same way Brutaka does with the Olmak; neither really pass through the shields in the way a Makuta would have to. This is why the Makuta are stuck in the death sphere when the storm starts.
If any of this is either already canon or contradicts canon make sure to correct me, not that you guys wouldn't jump on the chance already