Dispatches in the UK has a documentary on television tomorrow about the genetic problems due to marrying cousins.
TAZEEN AHMAD: Three of my uncles are deaf. Five aunts died as babies. Why? My grandparents were first cousins who married | Mail Online
If cousins cause so many problems today, think how bad it must have been in Antiquity. The Egyptian Pharoahs married half siblings (rather than full siblings) mostly; later the Ptolemies married full siblings, though children may also have been the products of secondary wives.
The Hecatomnids are attested as having married full sibling, and only Pixadorus the one that did not marry his sister is attested as having had a child (a daughter). The newly discovered Hecatomnus tomb is interesting as the sarcophagus depicts two children, and one has to wonder if they were his children or children of Artemisia II and Mausolus who died.
In the modern period we've seen how badly the Hapsburg Dynasty was affected by uncles marrying nieces, and cousins trying to pro-create.
Sheila Ager's paper "Familiarity Breeds: Incest and the Ptolemaic Dynasty" in the 2005 JHS seems to suggest that sibling marriage did not cause huge genetic problems amongst the Ptolemies. Having discussed this extensively with colleagues over the years, I would provide two reasons: some of the children were from secondary wives rather than the Isis-like sister-wife; and children with serious problems were almost certainly hidden away or discarded, as so few children are attested.