There is, however, an actual game play benefit to disabling animation, as it is one of the source of action delay (mind you not lag but delay), consumes more system resource on slower machines (which will cause lag) as well as block you from targeting for your next mystery.

So any smart and learned player will end up disabling it if it's optional and kind of defeat the purpose.

Frankly, the health issue is overstated. The chance of something happening is in directly correlation with the frequency of flash and have a correlation with certain colors. This game isn't bad enough, the pokemon case is extremely rare because you can hardly design a video sequence to be worse. That said, a warning would have been nice but it's really not as frequent a problem as people think.