The long haired breeds require more grooming. And trauma cases, like car accidents and fight wounds, are bad enough without the added complication of all that long hair caked with the stuff that comes with trauma. The bug eyed breeds are much more prone to eye injuries and diseases caused by the additional exposure of the eyes. Many of those breeds also have short little pug noses, and tend to make more noise breathing, and sometimes have serious respiratory problems. Poodles and yellow labs have more than their share of skin allergies.
Poodles also grow too much hair in their ears and sometimes get epilepsy.
Chihuahuas get hydrocephalus. Great Danes and St. Bernards bloat and get twisted stomachs. Springer spaniels tend to fracture their elbows, while labs, especially if they love to play Frisbee, tear ligaments in their knees. German Shepherds are prone to hip dysplasia. Dachshunds and Basset Hounds get back problems and the leg bones in the tiny little toy breeds are so thin that repairing fractures can be more expensive, and very difficult.