DoT isn't a big problem for a pihole, but it doesn't look like things are going that way. DoH can only be blocked by a mitm proxy. You would have to take a pretty serious security hit to do something like that with a pihole.
Sure, Apple (or whoever) could just bypass it and use something specific, but can already just use an IP, no DNS anyway?
IIRC, the vision with DoH is that eventually even browsers would do DNS as part of a bunch of pipelined HTTP requests. So you call up https://www.example.com/page.html and www.example.com resolves img.example.com for you since it's used on the page. The downside is www.example.com could also resolve tracker.adnetwork.com for you, too.
IIRC, DoH is there to defeat MITM attacks, but stuff like Pi-Hole is basically a MITM attack, so it's kinda collateral damage.
I bet network-level ad-blocking will eventually have to evolve into literal firewall rules on the gateway.