If you mean B.O. par 3's. they don't count for anything.
I think he means having the par 3 course count as your best 9 and 18 hole score. I agree that this is very silly. I know of players, well, one anyway, who played solidly for many hours in order to hit a genuine 49 at Kiawah. Being able to do it easily and have it show on your stats must be pretty crappy for those (very) few who have done it for real.
You're right in that they don't have any effect on your average but distance to hole, # of putts, birdies, bogies, eagles etc. all count.
Basically every stat counts, they just don't do anything to your average.