I have found a fix for this issue.
Most CAC enablers disable the macOS internal smart card reader. By re-enabling the internal smart card reader Safari will start prompting for a pin again. Follow these procedures to fix:
Check to see if internal smart card is disabled:
sudo defaults read /Library/Preferences/com.apple.security.smartcard.plist
If the following is present, then your internal smart card reader is disabled:
{
DisabledTokens = (
"com.apple.CryptoTokenKit.pivtoken"
);
}
To enable the internal smart card reader, then either modify the plist file and remove that section, or delete the plist file entirely:
sudo defaults delete /Library/Preferences/com.apple.security.smartcard DisabledTokens
or
sudo rm -f /Library/Preferences/com.apple.security.smartcard.plist (this is what I did)
Restart and try again.
Note: I have read that having the internal smart card reader enabled and using a CAC enabler can cause "other" issues. I am using CACKey middleware, and have not experienced any issues yet. If for some reason you do experience issues, the following command will restore the plist file as it was:
sudo defaults write /Library/Preferences/com.apple.security.smartcard DisabledTokens -array com.apple.CryptoTokenKit.pivtoken
Please reply with other solutions or issues if any, and of course if this fix worked for you.