We still would have easily found out had any of these methods been employed; any uncompromised machines still left in the country when they flipped the switch would start getting TLS warnings.
They could, of course, avoid spying on uncompromised machines to avoid detection, but then anyone practicing good security hygiene would be automatically left unaffected by the government spy program. Plus there'd still be the possibility of detecting malware through other means (malware on client machines is far easier to detect than MITM of unencrypted communications). Not to mention how much more difficult all this would be than simply MITMing unencrypted traffic.
The situation with HTTPS is significantly improved.
They could, of course, avoid spying on uncompromised machines to avoid detection, but then anyone practicing good security hygiene would be automatically left unaffected by the government spy program. Plus there'd still be the possibility of detecting malware through other means (malware on client machines is far easier to detect than MITM of unencrypted communications). Not to mention how much more difficult all this would be than simply MITMing unencrypted traffic.
The situation with HTTPS is significantly improved.