This is an interesting thread that I thought I'd chime in on.
I think when you consider whether or not to inbreed or line breed you have to consider what your goals are.
Typically, in a (zoo/public aquarium) managed population to goal is to maintain as much genetic diversity as possible for as long as possible. That managed population has a certain number of 'founders' which are basically your starter or wild caught animals that you initially start with. You want to try to breed them all roughly equally and minimize inbreeding as much as possible because that is how you maintain as much genetic diversity as possible over the long term. Your ability to do so is going to depend on the number of founders in the population- the more founders the easier it is to do.
Breeding for personal use is different I would imagine. I think there is much more interest in having rays that are seen as having a desirable pattern, or having other traits that the market likes. To do this, line or inbreeding can be valuable. That said, it can have negative consequences. You loose genetic diversity this way and fix traits. Those traits can be desirable like a really cool pattern, or undesirable like an animal with a health consequence. Some species seem to be more sensitive to inbreeding than others. There is not strong evidence that there have been health consequences in freshwater rays over several generations of inbreeding, but the more you do it the more likely you are to see it. You need to also consider your ability to outcross to unrelated individuals and if in 10 years many of these animals are no longer available from the wild that could be limited.
The question about inbreeding in the wild in interesting too. While it probably happens occasionally these are on the whole very large populations (especially compared to captive populations) that are found in large areas. I'd guess there isn't a whole lot of it.
