Both the Boulder CA software and the Let's Encrypt client fully support IPv6, and the majority (53%!) of traffic to the Let's Encrypt APIs is IPv6.
The problem is the validation piece due not to software development but rather datacenter connectivity. I've heard that it's been helpful to point the datacenter folks to all the discussion as a demonstration that IPv6 really is in demand.
(As a note, the selection criteria on the datacenter was driven far more by security requirements than IPv6 support. We figured we could encourage IPv6 adoption, as long as the security was top-notch.)