Coincidentally, SAIL Magazine just posted an article on this exact subject with Tom Cunliffe's solution that I've copied below:
When I bought my boat it had 18 through-hull fittings. To reduce the number of holes in the hull (I ultimately cut them by half), I first re-plumbed the drain hoses from my sinks, scuppers, bilge pumps and shower sump so that they could share many fewer outlets. I then removed the remaining unused fittings, feathered back the holes inside and out with an angle grinder, and filled them by layering on a succession of round fiberglass patches of increasing diameter.
I also reduced the number of intake seacocks to just two—one for the engine’s raw-water intake and one that I plumbed to a manifold that services every other appliance that uses seawater. On my boat this includes the galley sink foot pump, the toilet intake, the watermaker, the deck wash-down pump and a short bilge sump wash-down hose. I made my manifold from off-the-shelf PVC tubes and valves and installed a sea strainer between the seacock and the manifold. It has functioned perfectly for six years now.
Note that if you install a simple manifold, as opposed to a sea chest, to service multiple systems, the through-hull must be large enough to meet the likely maximum demand. A sea chest, which has a tank (capacity is typically a gallon or more), can more easily accommodate surge loads when more than one system is drawing water at the same time. —Tom Cunliffe--
SN68 Sangaris, Tropic Isle Harbor, FL