Packet loss over ICMP can be artificial based on the backplane load of routers, ACL's and artificial rate limits. They will de-prioritize responding to ICMP and fail to respond if CPU load is high but that does not mean the packets are not being forwarded 100%. Linux and BSD also have knobs for this behavior as well. HN is BSD.

Are you seeing TCP retransmits to port 443?

    for i in $(seq 69);do nc -vz -w1 news.ycombinator.com 443;sleep 2;done
    

Do that at the same time as watching

    watch -d -n4 --no-title 'nstat -a|grep -Ei "ret|los"'

It would be most useful to do this from your location and also from VM's on a few different providers in different locations to find which thing is not like the other. The 'nc' I am using is part of the nmap distribution. To force IPv6 replace the name with the IPv6 address.