despite Hera being a powerful goddess, SHE IS ALSO ZEUS'S SISTER. INCEST has a habit of WEAKENING the gene pool, hence Herc's greater abilities due to different (although mortal) genetics.
in one fantasy series I read in it the gods do not have genetics due to being beings of magic. So things like incest are not a problem from a genetic perspective. Obviously, in Marvel the gods have genetics of some sort. But the gods are also remarkably different. They can mate with things that by all right they should not be able to mate with and still produce offspring. Ares somehow produced horses. Zeus had a child born from his head. I wonder if something in the god nature prevents things like incest from effecting a child. At the very least it would be difficult to try and apply the same rules of human genetics to gods.