Yes, the certificate for the server is in the backup (it has to be otherwise the clients would refuse to connect to restored servers!)
We switched from MD5 to SHA many years ago so unless your backup is really old you won't have an issue.
People with MD5 are just noticing because they're officially dropping MD5 support in many clients. This includes the official openvpn client for windows (2.4.6) that you would download from the directly from them as well as some others like tunnelblick.
You can check your cert with:
sudo openssl x509 -text -noout -in /usr/share/untangle/settings/openvpn/server.crt | grep "Signature Algo"