Hakman has already given an excellent comment on why most of top players take the flag out and then put it back, since the shot is not affected.
Since I am not a great player, I never trusted my shots could be THAT close and hit the flagstick, but after this shot I'm going to share, I follow them and take the flag out, just in case.
This is how your first ever hole in one is denied:
http://www.wgt.com/replay.aspx?ID=766705cd-f1f1-41df-91c7-ac380188dcca
Peace,
Joel.