If the crust included the oceans, there wouldn't be different figures for the oceans in the same article.
You make a valid point about the seafloor being part of the crust; but I didn't intend to include the seafloor in "oceans".
> Atom count seems like a pretty pointless metric; we're talking about resources available for mining, in which case mass is what counts.
That depends on what we're mining the resource for. For example, if we're mining for metals to use in catalytic converters for vehicles, atom count is the relevant metric, since the catalytic effectiveness depends on the number of atoms, not on the total mass.