I bought a 28ft daytona this year and didn't know if it has 2 or 3 bilge pumps. Mine has an aftermarket plate in the center and I can't see if there is one. I am asking because my I pulled it out onto my trailer last week and when I pulled my plugs a lot of water came out of the center hull.

Hard to tell with your individual boat, but how many holes are in back of the boat to discharge out of? (the small billet fittings for the pumps)

You would have to have some way for the blidge pump to get the water out. More than likely if there is no water line coming out of the center section, than there is no pump.
My Daytona only has pumps in the sponsons none in the center pod. I put a plug in the drain in the engine room, that leads to the ski locker but you need to remue it if it rains and the boat is uncovered.
Your boat will hold water in the ski locker and the cabin if you do not drain the center pod.

My 2006 28 daytona has two pumps, but rarley does it get any water worth mentioning in it.(?)

Check why your boat had so much water in it, unless you were in some real rough stuff i guess.

My 2001 has 3 pumps and my friend's 1999 had 3.

As mentioned before, count the number of discharge holes.

My 02 30 had 2 I added a 3rd just for piece of mind.

My 06 28' has 2 in it.

33 has 3 pumps.

My 08 has two, one in each sponson.