Um...i can't be bothered to find the manga scan atm but i'm pretty sure we've seen a World Government ship coated and going to fishman island during the Queen Otihime flashback. To sign a treaty or something..can't remember 
Also, Smoker waiting above the sea is a smart move. As soon as a pirate ship floats back up, he can attack it as soon as possible using the element of surprise.
Then again, Trafalgar Law used to use a submarine ship so i reckon it wouldnt matter whether to get a ship coated or not because a submarine you don't have to worry about bubble popping . Btw, nice topic =D
It was a celestrial dragon one of those world nobles in OP that wanted its slaves that were taken away by Fisher Tiger. That was the only time we ever seen a world government ship coated... well those nobles are not actually the marine so snce the op was asking about marine ships I guess that is not considered..... So no marine ship has been seen coated. I can deduce many reasons about why we haven't.
1. Marine ships are heavier than normal ships they have that metal or stone called kairoseki embeded in ships... so it might be impossible for such ships to go undersea.
2. The Marines as the name says have submarines like Tral***ar Law's which they use to go underground. Like on that lastfiller where that guy who has two elbows (not sure if he's from long arm tribe) and followed Master Z. He used to be a Marine agent and he used submarines to launch an attack on the Marines csrring that big pan ossan... yeah that is enough to prove they have submarines.
3. But if they have submarines why haven't we seen them use them on any pirate or rather on the straw pirates? Answer is simple, the Marine style of fighting is to fight pirates directly, and using submarines is out of their fighting style. And you were right this is a nice topic.
