Depends what you're trying to get rid of - rainwater? waves shipping into a cockpit? or washdown residue?
Also the size of vessel and the type of sea it may encounter (if it's ocean-going).
For small pleasure boats (up to 50ft WL), I have seen a recommendation for draining enclosed cockpits based on one 2 inch drain for each 20 sq ft. I'm not sure this is enough if you're going to ship green water over an enclosed deck space - you can take on 3 or 4 tonnes of water in a single wave.
Why are you containing it in a holding tank? If it's washdown residue then you obviously don't need as much. I would still stick to 2 inch drains with smooth hose and gentle bends to enable blockages tro be cleared.
John