I think they do contribute to the S-matrix.The amplitude of disconnected diagrams is the product of the amplitudes of all disconnected pieces. For example, putting two connected 2-particle scattering diagrams will give you a 4-particle scattering process, but it's not that physically interesting because this process is not a "genuine" 4-particle process in the sense that it's really just two 2-particle scattering processes happening independently(and the jargon is "cluster-decomposed" process), so that it's best to study the connected pieces separately(these pieces correspond to the connected part of S-matrix). A good reference on this is Weinberg's QFT Vol1 chapter 4.
So in a word, disconnected diagrams do contribute to the S-matrix, but not the connected part of S-matrix(the second half of the sentence is a tautology if one uses connected diagram as the definition of "connected part of S-matrix", but it won't be a tautology if one uses Weinberg's recursive definition)