It is true that in certain circumstances that an abnormal percentage of black or red pigment, in certain species, can be associated with cancers. Indeed Xiphophorus (swordtails, platies and the rest of that genus) have been used in cancer research. Still look at all the black, red, black and red commercial strains in the hobby!

Only one Google hit of note (in the first bunch of many more) was relevant when I looked for [guppies "black eyes"]. Noted guppy breeder, Stephen Kwartler did note that he didn't breed youngsters with extra-ordinarily dark eyes. He also had a color goal - intriguingly neutral females and that may have been a part of the process.
http://www.ifga.org/articles/breeding4.htm

If you fry's eyes are all the same, don't worry about them. Maybe some concern is justified if there are a lot of differences between them. If fry (or eggs) are all the same, go with them.

I once collected a batch of albino gardneri eggs. As killie eggs go, eggs are supposed to get darker as the embryo develops. These eggs remained pretty colorless and I almost threw them out until (DOH)I recalled that they ARE albino. Also, about that time a little pink eye winked at me. ;)

Your perception of eye color is partly a matter of experience. Those who exclaim how tiny guppy fry are have never seen gourami, tetra or rainbow fry!  Sometimes one will wonder if there are any fry in a tank which the adults have been vacated from. Then the light will catch the surface right and suddenly there will be all these slivers of glass! :)

If they aren't mal-formed, enjoy them. They will probably be as normal as most guppies and more "normal" for the species, than most fish-heads. ;)

Still, you've got a bunch of us keeping an eye out for dark-eyed fry. I'm sure the question will stay with us for quite a while.