After an update of ca-certificates, it prints out:

• Messages for package app-misc/ca-certificates-20140223:

• Broken symlink for a certificate at /etc/ssl/certs/5f267794.0
• Broken symlink for a certificate at /etc/ssl/certs/ce026bf8.0
• Broken symlink for a certificate at /etc/ssl/certs/c692a373.0
• Broken symlink for a certificate at /etc/ssl/certs/9af9f759.0
• Broken symlink for a certificate at /etc/ssl/certs/2cfc4974.0
• Broken symlink for a certificate at /etc/ssl/certs/20d096ba.0
• Broken symlink for a certificate at /etc/ssl/certs/55a10908.0
• Broken symlink for a certificate at /etc/ssl/certs/03f0efa4.0
• Broken symlink for a certificate at /etc/ssl/certs/590d426f.0
• Broken symlink for a certificate at /etc/ssl/certs/99d0fa06.0
• You MUST remove the above broken symlinks
• Otherwise any SSL validation that use the directory may fail!
• To batch-remove them, run:
• find -L /etc/ssl/certs/ -type l -exec rm {} +

This is just a regular desktop system and it seems like ca-certificates should take care of maintaining these without requiring manual steps like this.