Please check that the Spam folder in Aqua Mail:
1) Points to this and same Spam folder on the server (there may be different ones there, Spam, Spam Messages, Junk Messages, Junk Mail, etc.)
2) Is set to "sync" so the app checks it as often as it checks the Inbox for example.
For this please:
1) Long press on the account -> options and folders -> folders
2) Let it refresh
3) Find the right spam folder (if there is more than one)
4) Tap its name, choose "Sync as spam"
5) Back out and now you'll have it on the app's main screen and it will be checked for mail (but won't notify).