Re: However if I delete on IMAP/EWS the deletion is synced with the server so if I change my mind I can still retrieve the message
The easy way to do this is to delete by "moving to the Deleted folder" which also happens to be the default "delete method" (out of three total).
And then you can open the Deleted folder, select your message(s) and use the "restore" icon to move them back.
Re: if I delete (from the server) with POP3 the email is permanently deleted. Is this correct.
With the default delete method, "move to Deleted" it works exactly same as described above, except for one thing:
Since POP3 does not provide access to server folders, this "moved to deleted" will only be reflected in AquaMail (i.e. the Deleted folder for POP3 accounts is always "device local").
In both cases, you can purge the Deleted folder (deleting all messages from the server) as a separate operation: 1) long press the Deleted folder, choose Delete All or 2) open the folder, Menu -> Delete all.
In both cases, you can open the Deleted folder, select some messages and move them back to the Inbox / source folder.