i don't think you got such "warnings" because something changed in HFS, but something changed with your security software.
If you use a security software that's designed to ask you for access to any kind of resource, then you are likely to be doomed to answer correctly to its questions.
About automatically defying such messages, I will look into that signing thing you suggested privately as soon as i get the time. I have still no idea on how much sweat and money it takes.
Other than this, i guess we can just report false positives.