Not sure if this would work, as I'm still very new both to modeling and particles.
Say the drain holes were individually modeled, with each one having the EffectChoices controller. The controller is set so that when the height of the drain hole is less than zero (in other words, has gone below the surface) it calls up a reference object which is a particle node. That particle node is the same drain hole but with the water streaming from it. That particle node would also have the VisibleUnderWater controller, with that set as false. That way, as long as the drain hole remains submerged you won't see anything. But as soon as it rises above the surface you'll see water streaming and draining.
If that particle generator is set to loop than it should keep invisibly replaying the draining water as long as the holes are submerged. Then, when the drain hole rises above water level, it should drain then stop. In calm weather you wouldn't see any draining. But, in rough weather, each time a wave washes over the hull and submerges the hole(s) it should start draining again once back above water.
Not sure if this would actually work and, alas, I'm way too new at this to try creating and testing it. So I thought I'd just toss this out here.
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