AquaMail's automatic setup for Gmail is IMAP, yes.
You can double check by long pressing on the account on the app's main screen -> options and folders -> you should see a sub-category "IMAP Options" and not "POP3 Options".
The Gmail "master switch" for IMAP is here:
https://mail.google.com/mail/u/0/?shva=1#settings/fwdandpop---
Now if that setting is off, then apps are not supposed to be able to use IMAP.
If AquaMail still works for you, despite, it's just a bug on Google's side, not because AquaMail uses any "tricks" or "magic"
So yes, I would make sure that the Gmail IMAP setting is ON -- who knows, the "off" may take effect unexpectedly and then Aqua would no longer be able to work with this account.