If the file is decrypted you need to use version 9 of HackingToolKit.... Pay attention to the name man. You need HackingToolKit3DS and you're using HackingToolKit9DS. Those are two completely separate releases. The former works with decrypted files, the latter ONLY works with encrypted ones.
So either use the 3DS version of hacking toolkit, or encrypt your .3DS and use the one you have. Either way, it's not the program failing it's a user error.