Animals ignore the emission of light from the flash.
I'm not certain I'd put all my marbles for that statement. The frogfish/scorpionfish yawn, many fish disappearing after the 1st flash, pygmy seahorses falling off perches etc, all indicate anecdotal evidence to the contrary. Many species rely on not moving to escape predators, so until someone puts an ECG/EEG/Stress meter on those things, I wouldn't assume too much either way.
I fully respect your experience but I'll put my experience against yours and say it's not conclusive at all. That is not to say what some ops are doing by banning strobes is correct but I also don't think flashing ANY subject that has eyes 1200 times is a good idea.
What appears to disturb the animal more than anything is the looming shape of the photographer especially if it obscures the light source (sunlight) and the actual noise (or the vibration) of the camera operating. Quite frankly, two Inon strobes discharged from a distance of a few inches seems to get no reaction whatsoever.
Sure, a big unfamiliar shape that looms around intimidates small fish. But you've been to Bali recently and dived the wreck. Like most sites where there is regular diving traffic, the fish don't react like the more remote reef denizens. Any creature with eyes will see the light emitted by the strobes, how it affects them is not certain just because they don't take off as if a predator is stalking them. I can say from my experience that when I edge up to some fish without lights, they are fine and then once I turn on the lights... gone! Maybe the lights illuminated my ugly mug and that scared them, but either way, it affected them.
If your guides are worried about the effect on the animals, tell them to get out of the water and take their divers with them! As for those polluting (diesel, sewage, noise) boats of your fleet....
That argument is the reason why the world is in such a mess. Either die and not pollute or do whatever you want? We know humans pollute. However, the dive ops are trying to preserve their ricebowl, which happens to be the undersea environment. Nothing wrong with protecting the reefs from errant divers or overzealous photographers who have crappy buoyancy etc. We do what we can.
We've all been to dive sites that have been ravaged by photographers and their guides who flip everything to find subjects (eg. the flying octopuses and boxer crabs on soft coral etc). I appreciate that you are trying to be the voice of reason to Emperor but a little overzealousness in protection is much better than lax enforcement and the resultant damage.
If they ban use of strobes on Emperor Dive boats, then they should tell you up front. Their choice and it's their customers to lose. Many liveaboards don't live off the photographer market anyhow so it's not that big a hit on revenues. I always ask if cameras/strobes are "encouraged" or not. If they say it is discouraged, then I can choose another ops. Otherwise, if they pull stuff like that once you are there, you just don't pay and/or tip and come to WP to tell others.