This bug appears to have started somewhere between 1.3-rolling-202006101523 and 1.3.1, but is still there in 1.4.2 and recent rolling releases.
The file /usr/share/vyos/templates/dhcp-client/ipv6.j2 is used as a template to generate the /run/dhcp6c/dhcp6c.pppoeX.conf file.
"set interfaces pppoe pppoeX ipv6 address autoconf" (and other config commands I have tried) does not generate the
" send ia-na 0;" and "id-assoc na 0 {" etc lines required for an ipv6 address on the pppoeX device.
the rest of the dhcp6c.conf config that generates the ipv6 prefix delegation addresses on other devices works.
Manually adjusting the template to generate the appropriate config causes pppoe to work OK.
The forum thread has more info https://forum.vyos.io/t/ipv6-does-not-seem-to-be-working-on-pppoe-interfaces-since-1-3rolling/16602