Possible xschem/ngspice weirdness #2: net voltages don't seem to be annotatable at lower levels of hierarchy if the net exists at a higher level. In the screenshot, nodes vim and vom do not annotate properly in the subcircuit, but do annotate at the top level. I took care to save the specific subcircuit nodes: .save V(x1.vim) V(x1.vom), but the spice_probe.sym instances do not annotate at that level.
This only seems to be true for the nodes which exist across hierarchy.