This will likely not be a problem with many reptiles that live their life within a limited area.
Many snakes spend their whole lives within ranges as small as a few square feet and these animals are already the result of years of inbreeding. The reason we are not currently seeing inbreeding depression in these animals is because the deleterious recessive genes have been "weeded out" thousands of years ago. In this case there really is no heterozygote advantage; however, in the wild, this low genetic diversity would not allow the animal to adapt to any disturbance and could prove to be detrimental. Obviously, in captivity this is not an issue.
I suppose problems may arise from inbreeding snake species that are highly genetically variable, in that genetic mixis takes place over great distances and populations are constantly introduced to novel genetic complements. Inbreeding these animals may lead to inbreeding depression because there are plenty of deleterious recessive genes that will be expressed in the homozygotes.
So, I suppose it depends on the animal, but as I had mentioned, snakes can get away with this as every species is generally the product of years of inbreeding in the wild anyway.
disclaimer: I certainly don't condone inbreeding in captivity when there is so much genetic stock out there to begin with, especially when were talking about the captive reptile industry.