No, nothing special as far as a hole goes. Eagle has the option of placing (unplated) holes or (plated) pads/vias. Both have an entry in the drill file.
I had to make the NPTH layer in the CAM processor. I'm not sure how I learned that including holes but not drills in the layer makes only the non-plated holes.
If the drill file shows them differently you may be able to just highlight which holes are unplated on a print and include it as a pdf.
Dealing with unplated holes in the fab house is a manual operation. All the holes are drilled, then the holes are plated. Non-plated holes are plugged during the plating operation so they don't get plated. The danger of a non-plated hole being plated is that there's no annulus for the plating to hole on to. During sussequent steps, any non-anchored bits of metal may break free and stick someplace else.
It is truly amazing how much work goes into making a 50 cent circuit board!