Yes, some hens will lay a glossier egg, with other having a more matte appearance. If your line has a good temperament, are vigorous, and have a healthy carcass, then I think you are in a good direction and should preserve those traits as much as possible.
There are few genetic diseases to worry about. The largest problem is decrease in overall vigor, but this occurs over many generations. If you mate a daughter to a father, for example, you will rarely see any genetic issues. Many breeders line breed, another word for inbreeding, to more accurately select for traits they wish to improve upon. A flock can stay closed to outside blood for many generations before needing a new outside bird (mainly due to the need to boost decreased vigor in offspring), but this is not to say you are breeding father to daughter, mother to son, or brother to sister for all those generations. You are often using two or three breeding pens and mixing offspring from those pens in the next generation. By breeding so closely to one another, you have less variables to fight when trying to improve your next generation of stock. With time, you come to know what is hiding in the genes of your flock and can make better breeding decisions. Adding in a new bird to the breeding pen brings that bird's entire genetic history with it, and many traits, such as white feathering in black birds, can pop up several generations down the road after the new bird is added.
This of course all gets rather serious in terms of space and record keeping, and many people are not so much interested in intense breeding. However I thought it would be a helpful explanation for mating closely related birds together.