One problem - at least for the project I'm working on - is that Lets Encrypt isn't a replacement for all of StartCom.
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