Any time the vertebrae are compressed or missing (correction -- any time something is compressed when it shouldn't be), there's a chance that the fish is suffering. It could be that the internal organs are pushed up against each other which could lead to anything from respiratory issues to trouble feeding.
For example, due to the compressed face of the English Bulldog, they often have respiratory issues, and are prone to simple things like... snoring really loudly. "These dogs are classified as brachycephalic dogs, or dogs with short snouts. This commonly results in compression of the upper jaw. Unfortunately, this is the cause for many respiratory problems in this breed. Nasal openings could be pinched or blocked, making breathing very difficult. Other respiratory issues could be attributed to narrow nostrils and windpipes."
And this is for a dog bred without any physical defects, aside from those inherent with the breed. I don't want to get into an ethics debate about breeding such an animal, I'm simply placing emphasis on the fact that these stubbys could very well be suffering.