This may be Eagle-specific terminology for what others call "Plated" and "Non-plated" holes - Consult the Eagle manual for clarification.
Normally, the holes for leads and pins of through-hole components will be plated - they will have a conductive "tube" inside the hole to provide connection between layers.
If you don't want this connection between layers, you have to specify the holes as non-plated. This will require a separate drilling operation, so the board shop will require a second drill file for the the non-plated holes (and will probably charge extra. Having the plated and non-plated holes on separate layers will facilitate making the separate drill files.