Yes go to alerts at the top right of your screen and click on it. At the bottom of the small page it will say Alert Preferences click that and you should be able to turn the emails off.
Button Quail are nice and small so you could keep them indoors. Cayuga ducklings are friendly and cute, but ducklings are very messy so I might not keep them inside.
Unfortunately I have seen them out during the day, as for why they left three alive I don't have a good guess. They may have just been playing with them, but I am not sure. Were there any tracks around your run or their pen?
Your problem may be a coyote. They can jump really high and climb the rest of the way up a fence, and they do live in Washington, so that may be him. Sorry about your Ducks I have a few myself and I would hate to loose them.