I doubt it takes any harm on the eyes, as you arent looking at it constantly.
It's not the eyes that are the problem. The real risks are neurological. Those stories about strobe lights and seizures are not urban legends. Over on another forum, one member was compelled to change his avatar* because people were getting migraines and actively avoiding threads he was involved with. One man had to pre-screen threads before letting his wife see them because she was seizure-prone. (This was in php/bb2, which doesn't have a suppress-avatars option.)
But even aside from the physical perils... do you really want to put something on your site that most people loathe intensely? If it's targeted at users under 17, sure, but otherwise it hardly seems worth the risk. Blinking may grab some people's attention and compel them to "watch that new link or text". It will make a sizable number of other people leave the page immediately, never to return.
* I think the People Up Top forcibly changed it and then allowed him to say it was his own decision. It was one of those swirling optical-illusion things.