Because of the current state Cocker Spaniels are in right now, I would suggest NOT breeding her. Cocker Spaniels are having MAJOR temperament problems right now and are currently the #1 biter in America and Canada. These temperament issues need to be worked out by the professionals who have been breeding this breed for years.
Failure to do this, in a few years will result in possible breed specific legislature which faces many breeds now. (the banning of a breed of dog)
Because of your dogs health problem, it could be passed onto the puppies. Not to mention that very often, problems with the thyroid also mean that there are other problems within the dogs body. We don't want to risk problems in the future for the pups and putting your dog through an unhealthy pregnancy.
You might want to visit
www.petfinder.org before you think about breeding your dog. There are currently over 100,000 pets on that site looking for home. Most are purebreds.