One of my highschool art teachers allways reminded his students to include "sky holes", as you call them, by saying that we need to remember to paint trees that the birds can fly through.
Right! Sky holes should fit seamlessly and convincingly into the scene. Also be sure there is a dark area on one edge representing internal shadow and that the edge not be uniformly hard. John F. Carlson also made a good case that sky holes should look darker than the general value of grass or sky behind the tree
Thanks for your comments!