How valid are Koestler’s criticism of evolutionary theory?
Maybe both. Certainly his understanding of limb developement doesn't match modern understanding. The quote you provide seems to indicate that he thought the appearance of an additional digit would require a multitude of coordinated mutations. Our current understanding seems to indicate that it's all about changes in the regulation of genes. For example in fruit flies mutations in the antennapedia gene can cause antenna to grow where legs should be or visa versa. Another example is polydactyly(extra toes) in cats which be be caused by mutations to a single regulatory region. 


  within a few generations, flies appear in the inbred ‘eyeless’ stock
  with eyes that are perfectly normal.


I'm not a fruit fly expert, but this seems highly dubious to me. There is a well studied eyeless mutation, but it's dominant, not recessive. Furthermore getting two copies of this mutant eyeless gene is lethal at the embryonic stage. This means that a colony of adult eyeless flys are necessarily all heterozygous. That is, they have one copy of the mutated eyeless gene, and one copy of the normal eyeless gene. By Mendel's laws, a quarter of the offspring from the completely eyeless generation are going to have two copies of the normal eyeless gene, and so will have normal eyes. I wouldn't be surprised if the flies with normal eyes outcompete the flies without eyes, so eventually the eyeless flies will disappear from the colony. I can't tell you whether Koestler has mis-characterized this gene, or is talking about some other gene all together. Citation needed.