Yes, we are very fortunate to have Let's Encrypt now.
We use a StartCom "MS Authenticode" certificate to sign our releases, so Windows users don't get a warning message from the various anti-malware scanners (and similar).
At first glance it sounds like Mozilla not accepting new StartCom cert's at some point won't affect that. It may snowball, but that's an unknown. o_O
ButI'm pretty sure Windows is not using NSS as its truststore for those checks. So its up to Microsoft to deal with the de-trusting (which may or may not be modular, I have no idea).
So I wish this would not affect the certificates StarCom issued for code signing.