With the default settings, a sound will only play if there is not an already posted notification, and only if the app received new messages during this particular mail sync.
You can change these in app settings under "Message notifications", turning off "Only when new messages", "Only when there are changes" and "Play sound only once".
Second thing to check -- per-account notification overrides. Long press an account -> special settings -> notifications.
Third -- do you perhaps have nighttime / weekend configured, forcing silent mode? This is in AquaMail settings, a few items below "Message notifications".