Yes, I can help.
In last night's update (1.4.0.27, July 4), icon counter/badge updates are disabled by default, so the launcher is still showing the number put there by the previous version, where it was enabled.
If you'd like to continue using the counter, please see app settings -> message notifications -> Launcher icon counter.
The reason was that someone reported compatibility issues on Android 4.1, Samsung's TouchWiz was crashing (those are manufacturer-specific, internal, undocumented functions, after all).
I apologize for the inconvenience. Bad judgement on my part.
Please check the setting I mentioned above.
It looks like I'll need to post another update tomorrow, enabling the counter by default again, but only for Android 4.2+, where no issues were reported.
You can also install this newer build, which already has this change.
http://www.aqua-mail.com/download/AquaMail-market-1.4.0.27.5.apkPS - This is only for Samsung / LG / Sony, where the code uses undocumented functions of those devices. Apex / Nova / Smart Launcher are not affected.
PPS - To disable the counter, use same setting. I'm attaching a screenshot.