If they're not shown at the URL opera://password-manager/passwords, they're gone. To restore them, you'd need a very-recent backup of your "Login Data" file in the profile folder (profile path is shown at the URL opera://about) or you'd need a CSV file you got from previously exporting your passwords.
If you were using Opera Sync and syncing passwords, you can goto https://www.sync.opera.com/ and see if the password count looks right. If so, there might have been a sync error. You can then try enabling Opera Sync and syncing passwords in a test standalone installation to see if it pulls in the passwords from the server. Then you could export them and import them into your regular Opera.
As for why it happened in the first place, unknown. But, if you're going to have to enter your usernames and passwords all over again, it'd be best to delete the "Login Data" file in the profile folder (while Opera is closed) first to start with a new one to make sure the file is not corrupted.