How to fix a through hole in stucco on the outside of the house?
The best way is to knock out enough stucco to find the studs, mount a backing plate to the studs, and stucco over that.  

Now, that's a lot of work, so there are quicker&amp; easier ways.  Perhaps you could cut a small plug out of plywood or similar material which press-fits each hole, then do a skim-coat over it to match the stucco.  

It comes down to time vs. quality, basically.