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I specifically asked about the health of the parents, to which the breeder said "they are great. hips are great but I dont have them certified becuase its really expensive."
That should have been your first clue. It isn't.

It also seems to me that I should get my dog fixed now to aid in getting this genetic defect out of the GSD blood lines....Does anybody know what the chance is that my dog will have it if his sister has it?
The short answer is yes, you should have him neutered. Hip dysplasia is at least partially genetic, but no one knows how much.

Oh, and by the way, my pup is checking out great. No signs yet. He is still young but his sister was already showing signs at this age. So that is encouraging. I've been feeding him NutroMax Natural Balance Large Breed Growth Control which allows him to grow a little slower and gives his bones and muscles a chance to devleope in hopes that it will prolong the onset of CHD. Does anybody know anything else I can do?
Hip dysplasia and hip pain are not the same thing. You probably can't do anything about the dysplasia (certainly not about the genetic component), but you can delay the signs. Studies done by Purina on Labadors showed that keeping the dogs a bit thin tremendously decreased the severity of SIGNS of hip dysplasia. There was also research in greyhounds that suggested increasing muscle mass on the rear legs also delayed development of signs, but that was never (to my knowledge) completed or published. Swimming is probably a good exercise. I have heard that every-other day exercise is good, but I don't think there's any actual research behind that recommendation.

There are also of course a number of surgeries, but hip replacement is the only one with good long-term results in a dog the size of a shepherd. It's expensive, but it works great.

Keep in mind that even radiographically confirmed dysplasia may not be clinically important. I had a Malamute with one hip OFA certified crappy, but she never developed serious issues and died at 12 of a brain tumor.
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