Yes, let's Encrypt will always attempt to resolve the domain and query the authoritive DNS server for answers.
I don't think let's Encrypt use cache for the domain IPs
Edit based on @ski192man
Let’s Encrypt doesn’t use anyone else’s recursive resolver but goes right to the source (making its own queries to the authoritative nameservers for the particular domain in question).
DNS Servers used by LetsEncrypt for Challenges - #6 by schoen