Do LEGO part counts on boxes include spare parts, brick separators and instruction manuals?
No. Set 30476 (pictured below) says it contains 33 pieces, but the set contains 3 extra pieces in addition to the ones needed to build the set. I believe it has always been this way.
Yes. When LEGO re-released the Taj Mahal, it contained exactly the same pieces except for the addition of a brick separator. The part count on the set's box was also increased by 1.
No, excluding the extra pieces, 30476 (pictured below) has exactly the 33 plastic pieces the manual says it should have.


Set 30476: