From the viewpoint of the repository (although, I am speaking primarily from the viewpoint of a university institutional repository), it would not be considered unethical or undesirable for authors to submit their work to more than one repository. Open repositories are built to increase access to the products of research and creativity, by making works publicly and freely available online. Submitting work to more than one repository is another way for an author to increase accessibility to his/her work.
The only copyright issue present would lie in the relationship between the author and the publisher that published the author's article. Most journals allow authors to deposit pre-prints of their work, that do not contain any edits or revisions from the publication process, in open repositories. Others allow authors to deposit pre-prints of their work that have been revised to show the revisions made in the publication process, and a few journals will allow authors to deposit the final publisher's version of the article. Some publishers will want their authors to wait a few months after publication before making their works accessible through open repositories.
Journals rely on the quality and originality of the articles they publish to build reputation. As most journals charge subscription fees, the originality of their articles is important. Open repositories do not operate on this model, so the ethics of publishing in journal do not translate to depositing your work in an open repository. Most repositories require their authors to sign a non-exclusive distribution license to deposit their work, which allows the repository to make the work accessible online. As a non-exclusive license, authors retain the right to submit their work to journals, other publications and other repositories.
Different open repositories have different functions. Institutional repositories capture the research and creative outputs of their host institutions. Subject-based repositories capture the the work being done in a specific field. Because repositories exist for different reasons, I would see no problem in submitting your work to multiple repositories.