In the FRR version the command has been changed
show ipv6 bgp
% Unknown command: show ipv6 bgp
with vtysh we can see that it should now be
show ip bgp ipv6
Also on a side note, it also seems that we should also use show ip bgp ipv4 to query the IPv4 address family although this is also the default when left out.
Moving the contents from /opt/vyatta/share/vyatta-op/templates/show/ipv6/bgp to /opt/vyatta/share/vyatta-op/templates/show/ip/bgp/ipv6 solved this part. However this needs more work since show ip bgp ipv6 neighbors is for instance not working correctly yet.