I haven't used POP3 with Aquamail myself, - so, I am guessing here:
I see that the number of messages in Inbox is exactly the same as in Deleted (4 and 4 for one account, 1 and 1 , for another). Since POP3 accounts do not have a concept of "Deleted" folder (or mail), - when you have "delete" configured in Aquamail as "move to deleted", it does so within the app, but doesn't delete the message until you expunge the message from Deleted. So, while Aquamail shows no messages in Inbox, it still reports the number of messages on the server.
You can test that hypothesis easily: just go to the "Deleted" account and empty it (there is a command for that there), and see if the message count for "Inbox" changes.
I see yet another account where you have 0 in Inbox, and several messages in Deleted. I am not sure if that is also a POP3 account, or an IMAP account, where it would work differently. Also, those messages could have been deleted from Sent.