The site says every Old Testament book except Esther is represented, then admits no verse of Nehemiah has been identified. Isn’t that a contradiction?

It is a real wrinkle in wording. Ezra-Nehemiah is one book in the Hebrew canon, so every book except Esther is defensible on a technicality, but a plain reader hears it as Nehemiah is there, and it is not. The accurate statement is that Nehemiah is unattested at Qumran apart from its pairing with Ezra. A small Nehemiah fragment has been reported from the antiquities market, but its provenance is disputed and the fragments once held by the Museum of the Bible proved to be modern forgeries, so nothing should be built on it.