Even in the case that it is compromised and you know it, your only option is certificate revocation. And you are in big trouble if you are relying on revocation because most clients do not keep very up to date with the CRL.
Not only for security, but the 90 days is to encourage automation. And most clients like certbot will check everyday, and if the cert is within 30 days of renewal, it attempts to renew. If letsencrypt is down, it will try again the next day. So you have an entire month before an outage would affect you.
No way. Every time I've worked with an organization with three years expiry it's guaranteed they have no idea, after three years how to even renew the cert. They are effectively longer in many cases than the hiring cycle and for larger organizations can be a complete nightmare. No one wants to invest in time in automation, training, tracking, etc., because it's so far down the road. The 90 day model makes much more sense because it requires automation. In terms of the ACME endpoints being down, I'm not going to say that won't happen but renewal starts 30 days before the cert expires and if Let's Encrypt's ACME endpoints are down for 30 days or longer there's a good chance we are all dealing with something far more dire than cert renewal at that point.
I have my own domain name servers, so it wasn't hard to wire up DNS-01 support.
Anyway, the client has been running daily out of a cron job, updating certs on remote servers as they need to be, with very little intervention from me, for well over a year now. It's just about a set-it-and-forget-it setup.
Let's Encrypt is intended to be fully automated and you shouldn't have to faff about with it every quarter, it should do its thing all by itself.
...most of the time.
1. Ubuntu VPS #1:
a. dovecot ssl
b. postfix ssl
c. apache multiple virtual domains ssl
d. pureftpd ssl
2. Ubuntu VPS #2:
a. apache multiple virtual domains ssl
3. Microsoft Server
a. IIS multiple virtual domains ssl
With Let's Encrypt, you don't need to minimize the number of certs just to save some money.