When you are saying "I've got my own domain", - where are you e-mails are hosted?
Some providers are automatically deleting the messages moved to "Spam" after certain amount of time (e.g. Gmail, Yahoo, ... ).
A few thoughts of what you might try.
1. You wrote that you "can't find any emails in the spam box". So, I assume you looked inside the
folder on your device. But just in case:
While you are in the message-list view, press on the pull-down "drawer" in the left top corner and choose "other folders". In that list, find the folder that has a designation "Spam, not synced" or "Synced as Spam". [I presume that where you've looked. If you haven't looked there yet, - check there.]
See if there is any other folder that might carry a similar name and that doesn't have that designation. (This is just in case your Aquamail has lost the correct "mapping" of its "Spam" folder with the folder's Spam folder, where previously marked-as-spam messages might still reside.
2. From the web-interface, take a look at what appears there as the "Spam" folder.