I'm gonna have to agree that it's more about the breeder than the size. Some breeders will find health issues in their pups but still breed their parents anyway because the pups are smaller.
My little one is 3 lbs and a year and a half. She has some mild skin allergies so she gets itchy a lot. She has recurrent anal gland problems, so she needs to have them expressed monthly- that's been going on pretty much from day one. She was diagnosed with luxating patella about 2 months ago, which is disappointing cuz we really tried hard to prevent that (even tho I guess it's not preventable, we tried to cut her risk by not letting her jump on/off furniture).
She is still young and her breeder was less than favorable as it turns out, so there could be more that develops. On paper, her health looks worse than it really is tho. We just had to put her on a specialty kibble for her skin, and have to keep an eye on her knee. She's still perfect to me!