The gene pool is very limited for some species. Some might rely on only a single founder plant. There are lots of reasons for this, the two main ones are probably CITES as mentioned (it can be difficult to get new plants into cultivation) and possibly more important, most people do not breed their orchids. So, very nice species may be in cultivation, but are never used in breeding so their genes do not get passed on.
Inbreeding is less of a problem for plants than animals. But not for the reason you think. Humans are generally considered less expendable than plants. Genetically inferior humans are usually not culled (for obvious reasons), but you get a lot of plants out of a cross and you should certainly cull the worst out. As a breeder you should expect that 90% of your efforts will be total garbage, and feel very lucky if you get a better percentage. A lot of plants won't even make it out of flask, if they have messed up genetics they won't grow very well. A lot of the remaining plants will be inferior. A very few of the plants will be superior, and those are the ones you breed with.
An old adage, you judge an orchid breeder by the size of his compost pile, not the number of plants in the greenhouse. Inferior plants should be destroyed, not given away or sold. The goals of your breeding program may vary, but when I screen plants (rarely, I don't do much hybridizing lately) I insist on vigor and ease of bloom as the primary factors. Flower quality is third. No point having a beautiful flower on a plant that won't grow. Anything that isn't vigorous and easy to bloom gets thrown away. Of the remainder, only the very best flowers are used for breeding, of course. That doesn't leave much.
For species, you get better odds. Most straight species crosses (selfings or outcrosses) give pretty good results. Most of the offspring will be satisfactory, and if the cross takes at all you usually have pretty high viability. Most primary hybrids (crosses between two species) give pretty predictable results. When you get farther away than that (selfing or crossing complex hybrids), all bets are off and you'd better have your pitchfork ready.
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