If the flooding hull is working correctly you shouldn't generally get any water on deck - it floods and fills a void beneath the deck. Yes it will sit a tiny bit lower in the water when flooded, but is still very buoyant and surrounded by tubes so shouldn't just start taking on water from every passing wave!
I've never had an issue with any SR's with flooding hulls - I'd certainly try it "as is" first before you start modifying anything.
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