what exactly are these holes for
 

I'm new to the fountain family so please put my ignorance aside. The holes in question are 2 thru hull fittings on a 29 fever in the hull just above the drain plugs on the bottom of the step up, and are connected with 1 1/4" hose to thru hull fittings on port and starboard next to the bilge discharge fittings. I'm thinking could they be to ventilate the hull and if so do they actually work. 2nd. guess was were they for thru hull water pickups if the boat had twins.

ventilate hull is the answer! you probably also have some ball valve to shut the aeration!

If they are on the "bottom" of the boat, they are to break suction from the notched transom (I think what you calling the step up). There is no ball valve ... usually there is only one of these fittings and it is plumbed direct from the thru hull fitting on the bottom, directly to a fitting out the side, near the bilge pump drains. They have been on the 29's since the mid 90's to the best of my knowledge. Regarding whether the actually work .... ??? I guess you could plug it and see if you notice any difference?

that's exactly where they are but like you said no ball valve but there are two of them was wondering if they can be used as thru hull water pickups

Pickups for what?

water pickups rather than thru the nose cone. I don't know if the thru hull fittings suck air or water that's why I'm askin'

They aid the boat getting on plane by reducing suction on the transom notch. They SHOULD have gate/ball valves on them for safety. Should the hose break/leak you want to be able to shutoff the incoming water torrent.

didn't appear to be ball valves but come spring there will be

47' triple with 3 holes and hoses no ball valves here.....I could never be able to reach down there to shut them off anyways.