No, AquaMail does not "mark messages as read" when it checks mail.
However:
Most mail servers will mark as read any messages fetched over POP3.
POP3 doesn't have read/unread sync, so that's not an issue for *the app using POP3*.
But if you've also got another mail app set up using IMAP -- then IMAP does provide read/unread sync, and the "marked read" state will sync into such mail app from the server.
What this means in practical terms:
- mixing IMAP and POP3 access to same account is a bad idea
- I would recommend using IMAP in all mail apps on all platforms (mobile and desktop).