When I was in Costa Rica this past January, a lot of guides were pretty anti-flash, especially those leading night hikes. And in some small reserves where there are night hikes every night, I understand that, to a degree. Of course, most of the guides were also still saying that baby vipers are more dangerous than adults, which has been widely debunked.
One of my guides, however, was OK with some flash, pointing out that having 4-8 high-intensity flashlights trained on the organism is likely much worse than a few flashes. I do use diffused flash in my night photography (pretty much all arthropods and herps, not birds) but try to not take too many photos. Although I confess to have at times used it more than I should have.
As to how much the flash affects the organisms, I haven’t been able to tell from my experiences.