Not sure if this is supposed to happen, but when I tried to clone a large area, it said the area was too big, at about 13000 blocks trying to be cloned. I checked on MCedit to see if the number of actual blocks (not air) was that many, but the block count was under 4096, and air was taking up the rest of the space. So, from what I can tell, it included the air blocks in the count, and said it was over the limit.
Here's my exact command:
/clone ~14 ~ ~2 ~-7 ~26 ~-19 ~-40 ~ ~-19 masked
The result:
[11:02:30] Too many blocks in the specified area (13068 > 4096)