That says they use a single database, as in a logical MySQL database. I don't see any claim that they use a single server. In fact, the title of the article you've linked suggests they use multiple.
https://letsencrypt.status.io/ shows a list of their servers, which look to be spread across three data centers (one "public", two "high availability").
Do we know if it shows cold spares? That's all I think is needed at a minimum to avoid the problems I'm talking about, and I doubt they would note those if they don't necessarily have a hostname.
