NetRadiant lacks symlink support in pk3 files
The issue has been reported already in another section (xonotic-maps.pk3dir#104 (closed)), but it looks like it's actually a NetRadiant issue.
NetRadiant doesn't support symlinks in pk3 files, thus the Texture browser and the 3D view complain about "shader image missing" for a few textures.
For example, with exx/floor-panel01 (/textures/exx/floor/floor_panel01.jpg is a symlink to ../../map_warfare/floor_panel.jpg):