If they have a "clock" icon next to them, they're extracted by AquaMail from your actual recent messages, not stored anywhere.
App settings -> composing and sending -> recent addresses -> turn off.
If they don't (have a "clock" icon) then they come from the phone's Contacts / People app.
Google pulls them from a few different sources, Google+ (circles, post comments even), Gmail (when you reply in their web mail, maybe the app too).
Aqua doesn't know or care "what" made them available in your phone's Contacts when it looks things up there.
PS - and yes, the FAQ does have more information.