Yes (sigh) it's true -- AquaMail isn't really aware of Gmail's "we don't have folders, we have labels" -- so it will show your messages the way Gmail "maps" them to IMAP folders, which may include duplicates (for things like All Mail, Important, Starred).
Not good, but I don't have a fix or even in a position to start thinking about it.
Another thing about message counters -- Gmail app and Gmail web mail are built around "conversations" and so their counters reflect the number of conversations, too, not messages.
AquaMail's counters everywhere (total, unread, in notifications, widgets) are *message* counts, not conversation counts.