Yup, what YJ said. Figurin' it easier to test the Ball in the Water stat rather than the ACE stat, I decided to sacrifice a couple of old, beat-up, BX-Ds to the WGT Golf Gods on the Best of Water Holes CTTH.
I started out with 36 balls in the water for all game types on my "Water Boy" award. (if all Callys that would be $42!!)
Played BofW CTTH and plunked one in the lake on #8 (noted Harbor Town ball magnet H2O) intentionally (ahem). I finished up on #9 and my Water Boy went up to 37. So yes Water Boy includes CTTHs.
Started another BofW CTTH and drowned one on #1, Played #2. Then restarted on the tee of #3.
Water Boy stat didn't change. Still at 37.
IMO, it is safe to assume a CTTH ACE won't register in stats unless you complete the round.