If it's the "Recents" tab:
Those messages are extracted from actual recent emails stored on the device, every time you bring up the contact picker.
Since AquaMail automatically trims its local message store over time -- when all messages containing those addresses are trimmed, the addresses will stop showing on the recent list.
If it's the "Contacts" tab:
Those are taken from system contacts and system contacts only.
I'm aware of cases like yours, where some contacts don't seem to exist (in Contacts app), but -- the Contacts tab takes its content from system contacts and system contacts only.
Maybe you could try Google Contacts on the web, to see if those mysterious addresses exist there:
http://contacts.google.com