Duh: I completely missed the ´smooth shading' toggle in the skin modifier options :-(
Ubuntu 15.04 64bits/ Nvidia GTX970
Short description of error
It is impossible to set the smooth shading attribute on a mesh that has a subdivision modifier on top of a akin modifier. Other combinations (for example a subdiv on top of a mirror modifier) work as expected. When clicking the smooth shading button multiple times on a mesh with either just the skin mod or with both, some changes in the apparent normals and geometry are visible that cycle with each click, but no smooth shading is visible.
Exact steps for others to reproduce the error
Add -> Mesh -> Cube
Add Modifier : Skin
Add Modifier : Subdivision surface
There is no effect,
Apply Skin Modifier
Now the smooth shading is applied.
Alternatively: load the attached .blend an click smooth shading: no smooth shading is applied, but clicking multiple times does change the modified mesh topology.