At the moment, the IPv4 AFI is activated by default for all peers, which is usually not desired for IPv6 peers.
vyos has set protocols bgp 123 parameters default no-ipv4-unicast but this doesn't seem to actually do anything other than add "bgp default ipv4-unicast" to the config, because "protocols bgp var neighbor var remote-as" automatically adds the activate line.
set protocols bgp 123 neighbor 2001:DB8::1 no-activate
This should then apply "no neighbor 2001:DB8::1 activate" to the neighbor
Ideally no-activate would be the default if no-ipv4-unicast was set.