When initializing a new GuixSD system with /home on an encrypted partition (as described in the manual), unprivileged users' home directories are not created.
I initialized the system with the encrypted partition locked and unmounted, but <kyamashita> from #guix had the same problem even though they had unlocked and mounted the partition. Of course, root can create the directories once the new system has booted, but none of the configuration files are there, which means the environment is not what is expected (my PATH was '/bin:/usr/bin'). I worked around the problem by removing my user from the operating system configuration, reconfiguring, putting my user back in the configuration, and reconfiguring again.