Run pihole -d for a new debug token. Have you installed Pi-hole without the web interface? Also, what is the result of those last commands but on a domain you whitelisted?
I had added coin-hive to the whitelist so it should have been on there. Its also affecting the supportxmr.com site among a few other sites on my whitelist.
If you answer all of my questions I would be able to pin down your issue better. Have you run pihole -g?
It looks like your upstreams may be blocking the domains:
Nov 17 14:47:17 dnsmasq[1446]: query[A] coin-hive.com from 192.168.1.1
Nov 17 14:47:17 dnsmasq[1446]: forwarded coin-hive.com to 127.0.0.4
Nov 17 14:47:17 dnsmasq[1446]: reply coin-hive.com is 0.0.0.0
I have not installed pi-hole without the web ui. If you don't see anything then maybe its the dnscrypt providers blocking those sites. After work I'll try and switch to a different dnscrypt provider and see if this issue persist.