Yes, duck[farm]s can become NPIP certified too. Every hatchery must be, or else they would not be allowed to ship into other states. The reason why i mentioned the "neighborhood-ducks" is that those mutt-ducks are often more healthy and more vigorous than over-clean-bread incestious ducks. My black Swedish ducks for example are the cutest, friendliest feather-balls on earth, but every day another one is limping and it is not always a drake's fault. Sometimes they just stumble over their own feet and limp on…
At the complete opposite scale are my Buff-Orpington/Runner muttlings: They have the
hybrid-vigor, are large, clever and know all too well how to wrap me around their webbed fingers, especially Mini Duck! - Which would make them really good pets. (imo)
But you're correct, with hatching eggs you never know what you get and may end up with all drakes…
Speaking of drakes: You cannot compare a drake with a rooster! Some drakes are rough to the girls when the hormones boil over in spring, but i have never seen a drake killing another drake. They brawl for a moment and then its done. And single drakes usually are very gentle with their girls, for example let them eat the treats first and just snack one or two. Drake sonly become a problem when there are not enough ducks around and they start to overbreed.