Yes, I disable it using the suggested method of returning NXDOMAIN for "use-application-dns.net". I do also disable it in applications such as the browser to avoid the log entries.

    grep appli /etc/unbound/unbound.conf 
     local-zone: "use-application-dns.net." always_nxdomain

And then I have about 80 IP's that I blackhole. People often counter that with, "but DoH can run on any HTTPS endpoint and you can't block CDN's", and whilst this is true I have never run across a CDN performing front-ending DoH and I am the type of person that will block a CDN. I can route HTTPS for specific applications through my own VPN mesh if it came to that and use Squid SSL Bump MiTM proxies to sanitize URL's which I have done in the past. It would just be a couple ACL's in Squid to block DoH end-points. The only domains I can not MiTM are those still using public key pinning such as Paypal which I will never use, eff.org, and a few Google sub-domains. There are probably a few others I have not run across on my Squid proxies.

As a side note, I think PiHole should consider adding a feature for Squid MiTM proxy mode so that more people can do this, with options like peeling off specific LAN clients to use the proxy or force everything through it.