We generally use that tool for determining how good a library preparation method was for an isolate of finite size. For a metagenome, by telling you what percent of the reads are unique as you continue to sequence, you can at least get an idea that... for every $1 I spend on additional sequence, $0.99 is spent on things I've already seen. But actually determining the total size of the metagenome from this kind of data is an open research area, and it's not clear to me if the "total size of a metagenome" is meaningful in the wild. So, I think the answer is that it's a little useful, but not a complete answer.
