Compromise of private CAs isn't always difficult. People store unencrypted keys on SharePoint or send them in email along with the password. There's also cases of rogue IT department staff using the private CA intended to be used for `*.corp` to MITM employee Internet traffic, so "compromise" isn't needed for harm to occur. For companies that do it right, yeah, the concern is minimal.
I think the risk of leaking internal domain names is real, but overblown. If you find a vulnerable internal service via CT logs you still need to connect to the private network to exploit it. If you're connected to the private network, you could have enumerated subdomains many other ways. Early knowledge of vulnerable subdomains can speed up an attack or target selection, but this is still a two step process. Most subdomains are pretty boring anyway; it's not surprising to learn that $corp has subdomains like webmail, wiki, etc. These names don't leak version or brand information.
I was playing with the idea of doing CT log poisoning, where you register and renew certificates for decoy subdomains along side your real subdomain names. If you add enough noise, CT logs are no longer useful for enumerating private subdomains.