It depends. Responsible breeders breed healthy dogs. Today we know about and can test for genetic diseases and breed away from them. My labrador is a carrier for EIC (exercise induced collapse.) Her sire had many desirable traits for field champion caliber labs. He was bred to an EIC clear female. So none of the pups will exhibit the condition. However, since we know my dog has the single gene for the recessive disease… we spayed her. We just want her for her superb retrieving traits.
All things being equal, a well bred pure bred should be healthier than a mutt of unknown heritage.
I will add, however, that there is no way to breed some dogs and end up with healthy off-spring. In particular, I refer to the dogs (bull dogs, pugs, etc.) with the mushed in faces where their ability to cool themselves is impaired.