an idea I had for a condition dragons with multiple heads could have is that they can be 'split', basically it causes them to hatch out as two separate dragons.
this tends to lead to one having organs the other doesn't. or having missing legs.
only in two-headed species this is not fatal. however it is still fatal in seashockers, as they are connected in a more unique way.
Fascinating and makes complete sense!
Some other genetic disorders that popped into my head from your ask:
Soft spines: Can affect any dragon but is detrimental to sharp class dragons. This can be caused by a severe calcium deficiency. Or by a genetic condition. The genetic condition can be deadly and can be "helped" but not cured, by an insanely high calcium diet.
Magma blockage: A rare genetic condition that leads to a deformation of a boulder class dragon's magma pipe. This usually leads to death in the wild. But with a friend and some help, it can be managed. Mostly via physically breaking up the blockage by hand or lava baths. (the heat from the lava helps melts the blockage.)
(A fire power blockage can happen to any dragon. Ice, acid, fire, etc.)
Gel blockage: This affect monstrous nightmares, cavern crashers, and other dragons with similar abilities. Gel blockage is incredibly painful and can eventually lead to infection. Due to all the scratching leaving open wounds. It can be caught early via Unusual gel color and a nasty smell. They itchiness and a complete ceasing of gel production. The dragon needs to soak in a hot spring till the problem goes away. Dragons naturally do this during nesting season to prevent this and other issues.
Wither wing: An issue when the baby is developing in the egg. This leads to the wings either being too small, deformed, or the webbing too weak for flight.
