Au contraire, mon frère fromage!
There are, in fact, large metal ships with limber holes. They're called submarines.
Submarines have a problem not faced by the boats above. Actually, they have a bunch of them, but let's stick to the one or two that are relevant. First of all, many submarines are composed of two hulls - a pressure hull and a light hull. In nearly all cases, the area between the light hull and the pressure hull is allowed to flood freely when the submarine submerges (which is the second specific problem the submarine has, namely that it will in the normal course of operation be entirely underwater).
When the submarine surfaces again, it is desirable for the spaces between the light hull and pressure hull to be allowed to drain themselves free of water. As a result, submarines with light hulls typically have one or more rows of limber holes along their sides above the waterline. This has been true for ages; look at any picture of a World War II submarine on the surface for an example. Modern U.S. nuclear submarines typically are single-hull above their waterline, but modern Soviet/Russian-designed submarines have visible limber holes.