Very important distinction here, the people being 'impacted' by this court order are end-users who decide to use Cloudflare's recursive DNS resolver (1.1.1.1 / 1.0.0.1 etc).
There's also the topic of what authoritative nameserver a domain uses. And also if a domain uses Cloudflare's WAF/CDN services to front their website.
A website can use Cloudflare's WAF/CDN without using their authoritative nameserver, and vice versa.
In this case, every domain that's been ordered to be blocked was already using Cloudflare's WAF/CDN service. So Cloudflare did the block at that level, rather than changing how Cloudflare's recursive DNS resolver responds to DNS queries.
No additional TLS certificates were issued - they already had valid certs because they're fronting the domain.