Patch Hole In HardiPlank Fiber Cement Siding

I don't think you'll be happy with spackle for anything bigger across than a nail hole. It's not very strong, and also not very sticky. So what tends to happen in your situation is that the spackle will fall through the hole into the wall; if not when you're applying it then it will be likely to do it when you try to sand it smooth before you paint.

I think the solution that's going to get you the best results for holes that size would be to cut a 2" square of fiberglass drywall joint tape and stick it over the hole, and then use joint compound to fill the hole and cover the tape, feathering it out to a 6-8" diameter circle. You can do this reasonably well with a cheap 4" putty knife. Then sand it smooth, being careful not to sand all the way through to the tape.

"If you have some small cracks and holes in your siding, you can fill them in with patching material specifically designed for this purpose, available at your local hardware store. Keep in mind that the patching will be obvious, whether or not you paint over it, so this is the best solution if the cracks and holes are in out of the way places that aren’t readily noticeable. If you have really big holes and cracks, then the siding will probably have to be replaced altogether."

Source: http://www.doityourself.com/stry/how-to-repair-fiber-cement-siding#b