Yes, they are visible to monitoring software; however, it is still secure.
Note that even if a hacker were to delete all these Alias Files, they still have to deal with the main license file, which is kept up to date with the state of the application. Also - as soon as the app is restarted and the ClientProtector can not find any aliases or the virgin installation key, the aliases are re-written. If instead of deleting them, they want to try and tamper with the files, they must first break the 512-bit encryption employed (not an easy task).