I agree that hypoxia is out. The water's deep, well-mixed, and offshore.
Localized algal bloom's quite possible, whether it be caused by dinophytes, diatoms, cyanophytes, or martian microbes. Usually specific algal groups have characteristic toxins... I wasn't aware Noctiluca even secreted appreciable amounts of it, but being a dinophyte it should carry some dinotoxins (that's what they do).
As for species-specific mortalities (Rick's last post), they can certainly be theorized to be viral/bacterial, but it very often is not the case. Every species has it's own catastrophic vulnerabilities to the odd toxin/chemical. A pile of sick/dead dogs for instance could be linked to CHOCOLATE, copepods will mass-suicide if even a LITTLE petroleum contaminates the water column, Diver X is violently allergic to neoprene, etc... When species or narrow taxa exhibit death or dramatic behavioral/physiological change to an environmental cue (be it chemical or physical), we call them "indicator species." Canaries in mineshafts are a popular example.
You can also have behaviorally induced mass mortalities, which also tend to target very specific taxa. Cetaceans beach en masse because the leader only is sick, or maybe just confused. Schooling bottom feeders like hardhead catfish and goatfishes could all pile up into a nepheloid reducing layer and get wiped out in a few minutes. Reef sharks could all chow down on a large fish carcass heavily biomagnified with dinotoxin and flop over dead.
You can still have mortalities due to illness. It's just nobody hardly ever verifies this. Distinguishing a rapid illness from poisoning is extremely difficult. It's a bit easier to measure the water column for nasty chemicals and run tox screens on commonly occurring nasties. And with sharks... well they're about as impervious to disease as any organism ever created. Remember that stupid shark cartilage craze?
I emailed an inquiry to Emma. Maybe she has more information (assuming the dive boat informed her office).
I Know! It's SEA LICE!