I tried installing Guix System maybe about a year ago, but had problems with LVM on LUKS with full-disk encryption and missing and outdated documentation. Has this situation changed?
I haven't done that setup but I know various people that use Guix (on the IRC channel) have an encrypted setup. I'm not sure their exact file structure, but it in general full disk encryption is supported; any issues should be bugs. You can always ask on the IRC channel to get a feel of what people have done and anything that might be tricky.