I've had a few boys, all fe the same extended family of piggies with fatty eye, and still have one. They never had any eye infections, and didn't seem any more prone to eye pokes, or things getting stuck in them than my other piggies. I've always bedded on newspaper, hemcore/aubiose and hay. I've also used paper based and fleece with them with no ill effect.
The only thing I have noticed with my fatty eye piggies is that when they go out on the grass, especially if there is tree blossom about they get watery eyes. But it doesn't seem to bother them.