Well, if they appear already marked read, then there won't be any notifications...
Is the account set up using IMAP?
To check: long press the account -> account setup -> Manual. You'll be looking at incoming server settings. There should be a disabled, but readable "IMAP" or "POP3" near the top of the screen.
If it's IMAP:
IMAP synchronizes read/unread state with the server. If the messages are coming in as already marked read, it means that's what AquaMail is getting from the server.
1 - If you have a desktop mail app accessing same account over POP3, please switch it to IMAP (you may need to re-create the account in this app).
Most mail services will mark a message read in web mail (and IMAP) if it's been accessed using POP3.
2 - If you don't, this could be an issue with Yahoo. I vaguely recall this type of read/unread state mismatch from someone else's bug report (which turned out to be a server side issue).
Please check that there are unread messages in web mail, then run this test in Aqua:
Long press the account -> "Diag: message dates" -> choose INBOX -> run to completion, email me the log file (you'll be prompted). With this log, I'll be able to tell if the server is reporting any messages as unread.