This is less to do with eye health as it does with photosensitive epilepsy (PSE):
Television has traditionally been the most common source of seizures in PSE. For patients with PSE, it is especially hazardous to view television in a dark room, at close range, or when the television is out of adjustment and is showing a rapidly flickering image (as when the horizontal hold is incorrectly adjusted). Modern digital television sets that cannot be maladjusted in this way and refresh the image on the screen at very high speed present less of a risk than older television sets.
Some PSE patients, especially children, may exhibit an uncontrollable fascination with television images that trigger seizures, to such an extent that it may be necessary to physically keep them away from television sets. Some patients (particularly those with cognitive impairments, although most PSE patients have no such impairments) self-induce seizures by waving their fingers in front of their eyes in front of bright light or by other means.
Since many anime contain rapidly flickering images (think flashing lights), the broadcasters ask to turn the lights on as it is especially hazardous in a dark room, for those susceptible.
This is happening even recently:
In some cases, specific television programs featuring certain types of visual stimuli have provoked seizures in a small minority of television viewers, including some viewers with no prior history of seizures of any kind. The "Dennō Senshi Porygon" episode of Pokémon is the most frequently cited example ... broadcast of the program in Japan, which includes strong flickering scenes, produced seizures in a surprising number of viewers, even though the proportion of viewers affected was extremely low
See the Public Responsibility section of the page for more examples.