There is a distinction between harm to the animals and harm to the dive experience. It looks like flashes don't physically harm the animals themselves. I am sure the same would be true for video lights.
But, the harm to the dive experience by disturbing the animals and causing them to flee is an whole different thing. The thresher sharks are a classic example. Given the rarity and expense of the dive, and the expense and effort just to get there, are the operators going to take the chance that flashes or video lights are going to cause the sharks to flee? Similarly, if lots of flashes causes a pygmy seahorse to want to move deeper into the sea fan, out of view, then it makes sense to limit how much irritation you can inflict on it.
Common sense needs to come into play. Classic example, there is an area near me where we can see sawfish. This is a new and very exciting discovery. I use a scooter with a camera mounted. But, before I went to the dive, I asked the operator if the scooter was OK or would it disturb the fish. He said they were very skittish and I should leave the scooter behind, which I did. I then asked, because of what he sais, if I should set up for wide angle or mid telephoto and he sald the latter. He was entirely right, the fish were very skittish and difficult to approach, and took off if you got within about 10 feet of them. Needless to say, gopro people were not welcome, either, needing to rush the fish just to get close enough. My mid telephoto setup was absolutely the proper thing. But, with the water conditions, it was not conducive to great photos with flashes, so I did not really get anything worthwhile as far as photos go. As far as the dive goes, it was amazing. Saw six of those things, one of the strangest big animals under the sea.
Sometimes, our desire to photo and video things must take a backseat to the dive itself. But, that has nothing with harm to the animals.