It depends if you want 2d or 3d holes.
If you want 2d holes, applied to a 2d surface then an opacity mask would be ok. This can be achieved if you apply a bitmap texture that has absolute 0 color. You can use the texture 12 (the red star) included as texture in Zbrush. This will allow to display the effect in Zbrush and all programs support this kind of opacity but translate to a traditional alpha.
You also could apply this as a mask as delete the faces but obvious would require lots of polys.
If you want a real 3d hole it depends what kind of object you was looking for and the solutions can vary a lot: noise, micromesh etc
https://www.youtube.com/watch?v=8xGlXLn_9bU
Also again you can mask with alpha and use extract, that will create a 3d surface with holes or whatever shape. This could be the simpler system.