Hi, I had the same issue and found a solution on Launchpad: https://bugs.launchpad.net/debian/+source/apache2/+bug/1665151
If the default Virtualhost doesn't contain old TLSv1.0 all Virtualhosts affected. I created a dummy on the 000-default-ssl.conf without cipher and SSLProtocol config and TLSv1.0 disapeared on all my other virtualhosts.
Best Regards, Tim