The issue primarily lies with loss of persistent connections, not downtime.
That’s changing the requirements to fit the implementation. A core goal of Let’s Encrypt is to make everything use TLS, and there’s no reason why legacy software (or software whose maintainers are unwilling to spend effort on hot-reloading) shouldn’t be in that list.
Virtually every IRCd, for example.
Frankly, having spoken to various IRCd developers over the years, I’d say that that’s extremely unlikely. The vast majority of them don’t appear to care for TLS at all, and it’s traditionally a culture in which user feedback isn’t really valued very much. I’m sure there are other ecosystems where the same applies.
It is exceedingly likely that IRCds will simply never come to support LE certificates, at all.
One of the principles you name isn’t quite accurate - the two principles at odds here are “automation” and “universally applied TLS”, not “free”. There’s a necessary tradeoff here - you can’t have both - and at this point Let’s Encrypt is favouring “automation” over “universally applied TLS”. I think that is a grave mistake.