Very few sites use certificate pinning. Chrome dropped support for dynamic certificate pinning. Web based certificate pinning is often recommended against because it's very hard to do right.

Also, using Let's Encrypt doesn't stop you from certificate pinning.

Certificate pinning (HPKP) is browsers is effectively dead, and was never a good idea to begin with.

There are far too many ways to self-DoS accidentally with HPKP. Also, an attacker who briefly gains control of your public DNS or web server can DoS a hostname semi-permanently.

If you’re talking about services that you’re accessing via a browser, true. If you actually do pinning (properly).

For service-to-service stuff and APIs the number of TLS clients that respect pinning is approximately zero.

Either way, the other problems remain, and running an internal PKI is really pretty easy.