Just one thought: does the Deleted folder get emptied in AquaMail (or appear to?), when you come back into the app?
If not, then please be sure to close AquaMail with Back, not Home (by Android convention, Home is like "minimizing" in Windows).
If it does and yet the messages don't get deleted from the server:
Please capture the issue in the app's debug log (see link below), with "raw session data" enabled.
Start with sending yourself a test message, checking mail in AquaMail (so the log captures how the message is received), then move to deleted, then exit letting the folder get emptied.
Send to kmansoft / gmail and I'll take a look.